` elements converts to PowerPoint shadows
+ - Supports outer shadows only (inset shadows are ignored to prevent corruption)
+ - Example: `
`
+ - Note: Inset/inner shadows are not supported by PowerPoint and will be skipped
+
+### Icons & Gradients
+
+- **CRITICAL: Never use CSS gradients (`linear-gradient`, `radial-gradient`)** - They don't convert to PowerPoint
+- **ALWAYS create gradient/icon PNGs FIRST using Sharp, then reference in HTML**
+- For gradients: Rasterize SVG to PNG background images
+- For icons: Rasterize react-icons SVG to PNG images
+- All visual effects must be pre-rendered as raster images before HTML rendering
+
+**Rasterizing Icons with Sharp:**
+
+```javascript
+const React = require('react');
+const ReactDOMServer = require('react-dom/server');
+const sharp = require('sharp');
+const { FaHome } = require('react-icons/fa');
+
+async function rasterizeIconPng(IconComponent, color, size = "256", filename) {
+ const svgString = ReactDOMServer.renderToStaticMarkup(
+ React.createElement(IconComponent, { color: `#${color}`, size: size })
+ );
+
+ // Convert SVG to PNG using Sharp
+ await sharp(Buffer.from(svgString))
+ .png()
+ .toFile(filename);
+
+ return filename;
+}
+
+// Usage: Rasterize icon before using in HTML
+const iconPath = await rasterizeIconPng(FaHome, "4472c4", "256", "home-icon.png");
+// Then reference in HTML:
+```
+
+**Rasterizing Gradients with Sharp:**
+
+```javascript
+const sharp = require('sharp');
+
+async function createGradientBackground(filename) {
+ const svg = `
`;
+
+ await sharp(Buffer.from(svg))
+ .png()
+ .toFile(filename);
+
+ return filename;
+}
+
+// Usage: Create gradient background before HTML
+const bgPath = await createGradientBackground("gradient-bg.png");
+// Then in HTML:
+```
+
+### Example
+
+```html
+
+
+
+
+
+
+
+
Recipe Title
+
+
Text with bold, italic, underline.
+
+
+
+
+
+
+
+```
+
+## Using the html2pptx Library
+
+### Dependencies
+
+These libraries have been globally installed and are available to use:
+- `pptxgenjs`
+- `playwright`
+- `sharp`
+
+### Basic Usage
+
+```javascript
+const pptxgen = require('pptxgenjs');
+const html2pptx = require('./html2pptx');
+
+const pptx = new pptxgen();
+pptx.layout = 'LAYOUT_16x9'; // Must match HTML body dimensions
+
+const { slide, placeholders } = await html2pptx('slide1.html', pptx);
+
+// Add chart to placeholder area
+if (placeholders.length > 0) {
+ slide.addChart(pptx.charts.LINE, chartData, placeholders[0]);
+}
+
+await pptx.writeFile('output.pptx');
+```
+
+### API Reference
+
+#### Function Signature
+```javascript
+await html2pptx(htmlFile, pres, options)
+```
+
+#### Parameters
+- `htmlFile` (string): Path to HTML file (absolute or relative)
+- `pres` (pptxgen): PptxGenJS presentation instance with layout already set
+- `options` (object, optional):
+ - `tmpDir` (string): Temporary directory for generated files (default: `process.env.TMPDIR || '/tmp'`)
+ - `slide` (object): Existing slide to reuse (default: creates new slide)
+
+#### Returns
+```javascript
+{
+ slide: pptxgenSlide, // The created/updated slide
+ placeholders: [ // Array of placeholder positions
+ { id: string, x: number, y: number, w: number, h: number },
+ ...
+ ]
+}
+```
+
+### Validation
+
+The library automatically validates and collects all errors before throwing:
+
+1. **HTML dimensions must match presentation layout** - Reports dimension mismatches
+2. **Content must not overflow body** - Reports overflow with exact measurements
+3. **CSS gradients** - Reports unsupported gradient usage
+4. **Text element styling** - Reports backgrounds/borders/shadows on text elements (only allowed on divs)
+
+**All validation errors are collected and reported together** in a single error message, allowing you to fix all issues at once instead of one at a time.
+
+### Working with Placeholders
+
+```javascript
+const { slide, placeholders } = await html2pptx('slide.html', pptx);
+
+// Use first placeholder
+slide.addChart(pptx.charts.BAR, data, placeholders[0]);
+
+// Find by ID
+const chartArea = placeholders.find(p => p.id === 'chart-area');
+slide.addChart(pptx.charts.LINE, data, chartArea);
+```
+
+### Complete Example
+
+```javascript
+const pptxgen = require('pptxgenjs');
+const html2pptx = require('./html2pptx');
+
+async function createPresentation() {
+ const pptx = new pptxgen();
+ pptx.layout = 'LAYOUT_16x9';
+ pptx.author = 'Your Name';
+ pptx.title = 'My Presentation';
+
+ // Slide 1: Title
+ const { slide: slide1 } = await html2pptx('slides/title.html', pptx);
+
+ // Slide 2: Content with chart
+ const { slide: slide2, placeholders } = await html2pptx('slides/data.html', pptx);
+
+ const chartData = [{
+ name: 'Sales',
+ labels: ['Q1', 'Q2', 'Q3', 'Q4'],
+ values: [4500, 5500, 6200, 7100]
+ }];
+
+ slide2.addChart(pptx.charts.BAR, chartData, {
+ ...placeholders[0],
+ showTitle: true,
+ title: 'Quarterly Sales',
+ showCatAxisTitle: true,
+ catAxisTitle: 'Quarter',
+ showValAxisTitle: true,
+ valAxisTitle: 'Sales ($000s)'
+ });
+
+ // Save
+ await pptx.writeFile({ fileName: 'presentation.pptx' });
+ console.log('Presentation created successfully!');
+}
+
+createPresentation().catch(console.error);
+```
+
+## Using PptxGenJS
+
+After converting HTML to slides with `html2pptx`, you'll use PptxGenJS to add dynamic content like charts, images, and additional elements.
+
+### ⚠️ Critical Rules
+
+#### Colors
+- **NEVER use `#` prefix** with hex colors in PptxGenJS - causes file corruption
+- ✅ Correct: `color: "FF0000"`, `fill: { color: "0066CC" }`
+- ❌ Wrong: `color: "#FF0000"` (breaks document)
+
+### Adding Images
+
+Always calculate aspect ratios from actual image dimensions:
+
+```javascript
+// Get image dimensions: identify image.png | grep -o '[0-9]* x [0-9]*'
+const imgWidth = 1860, imgHeight = 1519; // From actual file
+const aspectRatio = imgWidth / imgHeight;
+
+const h = 3; // Max height
+const w = h * aspectRatio;
+const x = (10 - w) / 2; // Center on 16:9 slide
+
+slide.addImage({ path: "chart.png", x, y: 1.5, w, h });
+```
+
+### Adding Text
+
+```javascript
+// Rich text with formatting
+slide.addText([
+ { text: "Bold ", options: { bold: true } },
+ { text: "Italic ", options: { italic: true } },
+ { text: "Normal" }
+], {
+ x: 1, y: 2, w: 8, h: 1
+});
+```
+
+### Adding Shapes
+
+```javascript
+// Rectangle
+slide.addShape(pptx.shapes.RECTANGLE, {
+ x: 1, y: 1, w: 3, h: 2,
+ fill: { color: "4472C4" },
+ line: { color: "000000", width: 2 }
+});
+
+// Circle
+slide.addShape(pptx.shapes.OVAL, {
+ x: 5, y: 1, w: 2, h: 2,
+ fill: { color: "ED7D31" }
+});
+
+// Rounded rectangle
+slide.addShape(pptx.shapes.ROUNDED_RECTANGLE, {
+ x: 1, y: 4, w: 3, h: 1.5,
+ fill: { color: "70AD47" },
+ rectRadius: 0.2
+});
+```
+
+### Adding Charts
+
+**Required for most charts:** Axis labels using `catAxisTitle` (category) and `valAxisTitle` (value).
+
+**Chart Data Format:**
+- Use **single series with all labels** for simple bar/line charts
+- Each series creates a separate legend entry
+- Labels array defines X-axis values
+
+**Time Series Data - Choose Correct Granularity:**
+- **< 30 days**: Use daily grouping (e.g., "10-01", "10-02") - avoid monthly aggregation that creates single-point charts
+- **30-365 days**: Use monthly grouping (e.g., "2024-01", "2024-02")
+- **> 365 days**: Use yearly grouping (e.g., "2023", "2024")
+- **Validate**: Charts with only 1 data point likely indicate incorrect aggregation for the time period
+
+```javascript
+const { slide, placeholders } = await html2pptx('slide.html', pptx);
+
+// CORRECT: Single series with all labels
+slide.addChart(pptx.charts.BAR, [{
+ name: "Sales 2024",
+ labels: ["Q1", "Q2", "Q3", "Q4"],
+ values: [4500, 5500, 6200, 7100]
+}], {
+ ...placeholders[0], // Use placeholder position
+ barDir: 'col', // 'col' = vertical bars, 'bar' = horizontal
+ showTitle: true,
+ title: 'Quarterly Sales',
+ showLegend: false, // No legend needed for single series
+ // Required axis labels
+ showCatAxisTitle: true,
+ catAxisTitle: 'Quarter',
+ showValAxisTitle: true,
+ valAxisTitle: 'Sales ($000s)',
+ // Optional: Control scaling (adjust min based on data range for better visualization)
+ valAxisMaxVal: 8000,
+ valAxisMinVal: 0, // Use 0 for counts/amounts; for clustered data (e.g., 4500-7100), consider starting closer to min value
+ valAxisMajorUnit: 2000, // Control y-axis label spacing to prevent crowding
+ catAxisLabelRotate: 45, // Rotate labels if crowded
+ dataLabelPosition: 'outEnd',
+ dataLabelColor: '000000',
+ // Use single color for single-series charts
+ chartColors: ["4472C4"] // All bars same color
+});
+```
+
+#### Scatter Chart
+
+**IMPORTANT**: Scatter chart data format is unusual - first series contains X-axis values, subsequent series contain Y-values:
+
+```javascript
+// Prepare data
+const data1 = [{ x: 10, y: 20 }, { x: 15, y: 25 }, { x: 20, y: 30 }];
+const data2 = [{ x: 12, y: 18 }, { x: 18, y: 22 }];
+
+const allXValues = [...data1.map(d => d.x), ...data2.map(d => d.x)];
+
+slide.addChart(pptx.charts.SCATTER, [
+ { name: 'X-Axis', values: allXValues }, // First series = X values
+ { name: 'Series 1', values: data1.map(d => d.y) }, // Y values only
+ { name: 'Series 2', values: data2.map(d => d.y) } // Y values only
+], {
+ x: 1, y: 1, w: 8, h: 4,
+ lineSize: 0, // 0 = no connecting lines
+ lineDataSymbol: 'circle',
+ lineDataSymbolSize: 6,
+ showCatAxisTitle: true,
+ catAxisTitle: 'X Axis',
+ showValAxisTitle: true,
+ valAxisTitle: 'Y Axis',
+ chartColors: ["4472C4", "ED7D31"]
+});
+```
+
+#### Line Chart
+
+```javascript
+slide.addChart(pptx.charts.LINE, [{
+ name: "Temperature",
+ labels: ["Jan", "Feb", "Mar", "Apr"],
+ values: [32, 35, 42, 55]
+}], {
+ x: 1, y: 1, w: 8, h: 4,
+ lineSize: 4,
+ lineSmooth: true,
+ // Required axis labels
+ showCatAxisTitle: true,
+ catAxisTitle: 'Month',
+ showValAxisTitle: true,
+ valAxisTitle: 'Temperature (°F)',
+ // Optional: Y-axis range (set min based on data range for better visualization)
+ valAxisMinVal: 0, // For ranges starting at 0 (counts, percentages, etc.)
+ valAxisMaxVal: 60,
+ valAxisMajorUnit: 20, // Control y-axis label spacing to prevent crowding (e.g., 10, 20, 25)
+ // valAxisMinVal: 30, // PREFERRED: For data clustered in a range (e.g., 32-55 or ratings 3-5), start axis closer to min value to show variation
+ // Optional: Chart colors
+ chartColors: ["4472C4", "ED7D31", "A5A5A5"]
+});
+```
+
+#### Pie Chart (No Axis Labels Required)
+
+**CRITICAL**: Pie charts require a **single data series** with all categories in the `labels` array and corresponding values in the `values` array.
+
+```javascript
+slide.addChart(pptx.charts.PIE, [{
+ name: "Market Share",
+ labels: ["Product A", "Product B", "Other"], // All categories in one array
+ values: [35, 45, 20] // All values in one array
+}], {
+ x: 2, y: 1, w: 6, h: 4,
+ showPercent: true,
+ showLegend: true,
+ legendPos: 'r', // right
+ chartColors: ["4472C4", "ED7D31", "A5A5A5"]
+});
+```
+
+#### Multiple Data Series
+
+```javascript
+slide.addChart(pptx.charts.LINE, [
+ {
+ name: "Product A",
+ labels: ["Q1", "Q2", "Q3", "Q4"],
+ values: [10, 20, 30, 40]
+ },
+ {
+ name: "Product B",
+ labels: ["Q1", "Q2", "Q3", "Q4"],
+ values: [15, 25, 20, 35]
+ }
+], {
+ x: 1, y: 1, w: 8, h: 4,
+ showCatAxisTitle: true,
+ catAxisTitle: 'Quarter',
+ showValAxisTitle: true,
+ valAxisTitle: 'Revenue ($M)'
+});
+```
+
+### Chart Colors
+
+**CRITICAL**: Use hex colors **without** the `#` prefix - including `#` causes file corruption.
+
+**Align chart colors with your chosen design palette**, ensuring sufficient contrast and distinctiveness for data visualization. Adjust colors for:
+- Strong contrast between adjacent series
+- Readability against slide backgrounds
+- Accessibility (avoid red-green only combinations)
+
+```javascript
+// Example: Ocean palette-inspired chart colors (adjusted for contrast)
+const chartColors = ["16A085", "FF6B9D", "2C3E50", "F39C12", "9B59B6"];
+
+// Single-series chart: Use one color for all bars/points
+slide.addChart(pptx.charts.BAR, [{
+ name: "Sales",
+ labels: ["Q1", "Q2", "Q3", "Q4"],
+ values: [4500, 5500, 6200, 7100]
+}], {
+ ...placeholders[0],
+ chartColors: ["16A085"], // All bars same color
+ showLegend: false
+});
+
+// Multi-series chart: Each series gets a different color
+slide.addChart(pptx.charts.LINE, [
+ { name: "Product A", labels: ["Q1", "Q2", "Q3"], values: [10, 20, 30] },
+ { name: "Product B", labels: ["Q1", "Q2", "Q3"], values: [15, 25, 20] }
+], {
+ ...placeholders[0],
+ chartColors: ["16A085", "FF6B9D"] // One color per series
+});
+```
+
+### Adding Tables
+
+Tables can be added with basic or advanced formatting:
+
+#### Basic Table
+
+```javascript
+slide.addTable([
+ ["Header 1", "Header 2", "Header 3"],
+ ["Row 1, Col 1", "Row 1, Col 2", "Row 1, Col 3"],
+ ["Row 2, Col 1", "Row 2, Col 2", "Row 2, Col 3"]
+], {
+ x: 0.5,
+ y: 1,
+ w: 9,
+ h: 3,
+ border: { pt: 1, color: "999999" },
+ fill: { color: "F1F1F1" }
+});
+```
+
+#### Table with Custom Formatting
+
+```javascript
+const tableData = [
+ // Header row with custom styling
+ [
+ { text: "Product", options: { fill: { color: "4472C4" }, color: "FFFFFF", bold: true } },
+ { text: "Revenue", options: { fill: { color: "4472C4" }, color: "FFFFFF", bold: true } },
+ { text: "Growth", options: { fill: { color: "4472C4" }, color: "FFFFFF", bold: true } }
+ ],
+ // Data rows
+ ["Product A", "$50M", "+15%"],
+ ["Product B", "$35M", "+22%"],
+ ["Product C", "$28M", "+8%"]
+];
+
+slide.addTable(tableData, {
+ x: 1,
+ y: 1.5,
+ w: 8,
+ h: 3,
+ colW: [3, 2.5, 2.5], // Column widths
+ rowH: [0.5, 0.6, 0.6, 0.6], // Row heights
+ border: { pt: 1, color: "CCCCCC" },
+ align: "center",
+ valign: "middle",
+ fontSize: 14
+});
+```
+
+#### Table with Merged Cells
+
+```javascript
+const mergedTableData = [
+ [
+ { text: "Q1 Results", options: { colspan: 3, fill: { color: "4472C4" }, color: "FFFFFF", bold: true } }
+ ],
+ ["Product", "Sales", "Market Share"],
+ ["Product A", "$25M", "35%"],
+ ["Product B", "$18M", "25%"]
+];
+
+slide.addTable(mergedTableData, {
+ x: 1,
+ y: 1,
+ w: 8,
+ h: 2.5,
+ colW: [3, 2.5, 2.5],
+ border: { pt: 1, color: "DDDDDD" }
+});
+```
+
+### Table Options
+
+Common table options:
+- `x, y, w, h` - Position and size
+- `colW` - Array of column widths (in inches)
+- `rowH` - Array of row heights (in inches)
+- `border` - Border style: `{ pt: 1, color: "999999" }`
+- `fill` - Background color (no # prefix)
+- `align` - Text alignment: "left", "center", "right"
+- `valign` - Vertical alignment: "top", "middle", "bottom"
+- `fontSize` - Text size
+- `autoPage` - Auto-create new slides if content overflows
\ No newline at end of file
diff --git a/scientific-skills/document-skills/pptx/ooxml.md b/scientific-skills/document-skills/pptx/ooxml.md
new file mode 100644
index 0000000..951b3cf
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml.md
@@ -0,0 +1,427 @@
+# Office Open XML Technical Reference for PowerPoint
+
+**Important: Read this entire document before starting.** Critical XML schema rules and formatting requirements are covered throughout. Incorrect implementation can create invalid PPTX files that PowerPoint cannot open.
+
+## Technical Guidelines
+
+### Schema Compliance
+- **Element ordering in `
`**: ``, ``, ``
+- **Whitespace**: Add `xml:space='preserve'` to `` elements with leading/trailing spaces
+- **Unicode**: Escape characters in ASCII content: `"` becomes `“`
+- **Images**: Add to `ppt/media/`, reference in slide XML, set dimensions to fit slide bounds
+- **Relationships**: Update `ppt/slides/_rels/slideN.xml.rels` for each slide's resources
+- **Dirty attribute**: Add `dirty="0"` to `` and `` elements to indicate clean state
+
+## Presentation Structure
+
+### Basic Slide Structure
+```xml
+
+
+
+
+ ...
+ ...
+
+
+
+
+```
+
+### Text Box / Shape with Text
+```xml
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Slide Title
+
+
+
+
+```
+
+### Text Formatting
+```xml
+
+
+
+ Bold Text
+
+
+
+
+
+ Italic Text
+
+
+
+
+
+ Underlined
+
+
+
+
+
+
+
+
+
+ Highlighted Text
+
+
+
+
+
+
+
+
+
+ Colored Arial 24pt
+
+
+
+
+
+
+
+
+
+ Formatted text
+
+```
+
+### Lists
+```xml
+
+
+
+
+
+
+ First bullet point
+
+
+
+
+
+
+
+
+
+ First numbered item
+
+
+
+
+
+
+
+
+
+ Indented bullet
+
+
+```
+
+### Shapes
+```xml
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+```
+
+### Images
+```xml
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+```
+
+### Tables
+```xml
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Cell 1
+
+
+
+
+
+
+
+
+
+
+ Cell 2
+
+
+
+
+
+
+
+
+
+```
+
+### Slide Layouts
+
+```xml
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+```
+
+## File Updates
+
+When adding content, update these files:
+
+**`ppt/_rels/presentation.xml.rels`:**
+```xml
+
+
+```
+
+**`ppt/slides/_rels/slide1.xml.rels`:**
+```xml
+
+
+```
+
+**`[Content_Types].xml`:**
+```xml
+
+
+
+```
+
+**`ppt/presentation.xml`:**
+```xml
+
+
+
+
+```
+
+**`docProps/app.xml`:** Update slide count and statistics
+```xml
+2
+10
+50
+```
+
+## Slide Operations
+
+### Adding a New Slide
+When adding a slide to the end of the presentation:
+
+1. **Create the slide file** (`ppt/slides/slideN.xml`)
+2. **Update `[Content_Types].xml`**: Add Override for the new slide
+3. **Update `ppt/_rels/presentation.xml.rels`**: Add relationship for the new slide
+4. **Update `ppt/presentation.xml`**: Add slide ID to ``
+5. **Create slide relationships** (`ppt/slides/_rels/slideN.xml.rels`) if needed
+6. **Update `docProps/app.xml`**: Increment slide count and update statistics (if present)
+
+### Duplicating a Slide
+1. Copy the source slide XML file with a new name
+2. Update all IDs in the new slide to be unique
+3. Follow the "Adding a New Slide" steps above
+4. **CRITICAL**: Remove or update any notes slide references in `_rels` files
+5. Remove references to unused media files
+
+### Reordering Slides
+1. **Update `ppt/presentation.xml`**: Reorder `` elements in ``
+2. The order of `` elements determines slide order
+3. Keep slide IDs and relationship IDs unchanged
+
+Example:
+```xml
+
+
+
+
+
+
+
+
+
+
+
+
+
+```
+
+### Deleting a Slide
+1. **Remove from `ppt/presentation.xml`**: Delete the `` entry
+2. **Remove from `ppt/_rels/presentation.xml.rels`**: Delete the relationship
+3. **Remove from `[Content_Types].xml`**: Delete the Override entry
+4. **Delete files**: Remove `ppt/slides/slideN.xml` and `ppt/slides/_rels/slideN.xml.rels`
+5. **Update `docProps/app.xml`**: Decrement slide count and update statistics
+6. **Clean up unused media**: Remove orphaned images from `ppt/media/`
+
+Note: Don't renumber remaining slides - keep their original IDs and filenames.
+
+
+## Common Errors to Avoid
+
+- **Encodings**: Escape unicode characters in ASCII content: `"` becomes `“`
+- **Images**: Add to `ppt/media/` and update relationship files
+- **Lists**: Omit bullets from list headers
+- **IDs**: Use valid hexadecimal values for UUIDs
+- **Themes**: Check all themes in `theme` directory for colors
+
+## Validation Checklist for Template-Based Presentations
+
+### Before Packing, Always:
+- **Clean unused resources**: Remove unreferenced media, fonts, and notes directories
+- **Fix Content_Types.xml**: Declare ALL slides, layouts, and themes present in the package
+- **Fix relationship IDs**:
+ - Remove font embed references if not using embedded fonts
+- **Remove broken references**: Check all `_rels` files for references to deleted resources
+
+### Common Template Duplication Pitfalls:
+- Multiple slides referencing the same notes slide after duplication
+- Image/media references from template slides that no longer exist
+- Font embedding references when fonts aren't included
+- Missing slideLayout declarations for layouts 12-25
+- docProps directory may not unpack - this is optional
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diff --git a/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd
new file mode 100644
index 0000000..6454ef9
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd
@@ -0,0 +1,1499 @@
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diff --git a/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd
new file mode 100644
index 0000000..afa4f46
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd
@@ -0,0 +1,146 @@
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diff --git a/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd
new file mode 100644
index 0000000..64e66b8
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd
@@ -0,0 +1,1085 @@
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diff --git a/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd
new file mode 100644
index 0000000..687eea8
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd
@@ -0,0 +1,11 @@
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diff --git a/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd
new file mode 100644
index 0000000..6ac81b0
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd
@@ -0,0 +1,3081 @@
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diff --git a/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd
new file mode 100644
index 0000000..1dbf051
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd
@@ -0,0 +1,23 @@
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diff --git a/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd
new file mode 100644
index 0000000..f1af17d
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd
@@ -0,0 +1,185 @@
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diff --git a/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd
new file mode 100644
index 0000000..0a185ab
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd
@@ -0,0 +1,287 @@
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diff --git a/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd
new file mode 100644
index 0000000..14ef488
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd
@@ -0,0 +1,1676 @@
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diff --git a/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd
new file mode 100644
index 0000000..c20f3bf
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd
@@ -0,0 +1,28 @@
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diff --git a/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd
new file mode 100644
index 0000000..ac60252
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd
@@ -0,0 +1,144 @@
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diff --git a/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd
new file mode 100644
index 0000000..424b8ba
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd
@@ -0,0 +1,174 @@
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diff --git a/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd
new file mode 100644
index 0000000..2bddce2
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd
@@ -0,0 +1,25 @@
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diff --git a/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd
new file mode 100644
index 0000000..8a8c18b
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd
@@ -0,0 +1,18 @@
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diff --git a/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd
new file mode 100644
index 0000000..5c42706
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd
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diff --git a/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd
new file mode 100644
index 0000000..853c341
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd
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diff --git a/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd
new file mode 100644
index 0000000..da835ee
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd
@@ -0,0 +1,195 @@
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diff --git a/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-math.xsd b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-math.xsd
new file mode 100644
index 0000000..87ad265
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-math.xsd
@@ -0,0 +1,582 @@
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diff --git a/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd
new file mode 100644
index 0000000..9e86f1b
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd
@@ -0,0 +1,25 @@
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diff --git a/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd
new file mode 100644
index 0000000..d0be42e
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd
@@ -0,0 +1,4439 @@
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diff --git a/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd
new file mode 100644
index 0000000..8821dd1
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd
@@ -0,0 +1,570 @@
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diff --git a/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd
new file mode 100644
index 0000000..ca2575c
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd
@@ -0,0 +1,509 @@
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diff --git a/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd
new file mode 100644
index 0000000..dd079e6
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd
@@ -0,0 +1,12 @@
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diff --git a/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd
new file mode 100644
index 0000000..3dd6cf6
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd
@@ -0,0 +1,108 @@
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diff --git a/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd
new file mode 100644
index 0000000..f1041e3
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd
@@ -0,0 +1,96 @@
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diff --git a/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd
new file mode 100644
index 0000000..9c5b7a6
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd
@@ -0,0 +1,3646 @@
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diff --git a/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd
new file mode 100644
index 0000000..0f13678
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd
@@ -0,0 +1,116 @@
+
+
+
+
+
+ See http://www.w3.org/XML/1998/namespace.html and
+ http://www.w3.org/TR/REC-xml for information about this namespace.
+
+ This schema document describes the XML namespace, in a form
+ suitable for import by other schema documents.
+
+ Note that local names in this namespace are intended to be defined
+ only by the World Wide Web Consortium or its subgroups. The
+ following names are currently defined in this namespace and should
+ not be used with conflicting semantics by any Working Group,
+ specification, or document instance:
+
+ base (as an attribute name): denotes an attribute whose value
+ provides a URI to be used as the base for interpreting any
+ relative URIs in the scope of the element on which it
+ appears; its value is inherited. This name is reserved
+ by virtue of its definition in the XML Base specification.
+
+ lang (as an attribute name): denotes an attribute whose value
+ is a language code for the natural language of the content of
+ any element; its value is inherited. This name is reserved
+ by virtue of its definition in the XML specification.
+
+ space (as an attribute name): denotes an attribute whose
+ value is a keyword indicating what whitespace processing
+ discipline is intended for the content of the element; its
+ value is inherited. This name is reserved by virtue of its
+ definition in the XML specification.
+
+ Father (in any context at all): denotes Jon Bosak, the chair of
+ the original XML Working Group. This name is reserved by
+ the following decision of the W3C XML Plenary and
+ XML Coordination groups:
+
+ In appreciation for his vision, leadership and dedication
+ the W3C XML Plenary on this 10th day of February, 2000
+ reserves for Jon Bosak in perpetuity the XML name
+ xml:Father
+
+
+
+
+ This schema defines attributes and an attribute group
+ suitable for use by
+ schemas wishing to allow xml:base, xml:lang or xml:space attributes
+ on elements they define.
+
+ To enable this, such a schema must import this schema
+ for the XML namespace, e.g. as follows:
+ <schema . . .>
+ . . .
+ <import namespace="http://www.w3.org/XML/1998/namespace"
+ schemaLocation="http://www.w3.org/2001/03/xml.xsd"/>
+
+ Subsequently, qualified reference to any of the attributes
+ or the group defined below will have the desired effect, e.g.
+
+ <type . . .>
+ . . .
+ <attributeGroup ref="xml:specialAttrs"/>
+
+ will define a type which will schema-validate an instance
+ element with any of those attributes
+
+
+
+ In keeping with the XML Schema WG's standard versioning
+ policy, this schema document will persist at
+ http://www.w3.org/2001/03/xml.xsd.
+ At the date of issue it can also be found at
+ http://www.w3.org/2001/xml.xsd.
+ The schema document at that URI may however change in the future,
+ in order to remain compatible with the latest version of XML Schema
+ itself. In other words, if the XML Schema namespace changes, the version
+ of this document at
+ http://www.w3.org/2001/xml.xsd will change
+ accordingly; the version at
+ http://www.w3.org/2001/03/xml.xsd will not change.
+
+
+
+
+
+ In due course, we should install the relevant ISO 2- and 3-letter
+ codes as the enumerated possible values . . .
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ See http://www.w3.org/TR/xmlbase/ for
+ information about this attribute.
+
+
+
+
+
+
+
+
+
+
diff --git a/scientific-skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd b/scientific-skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd
new file mode 100644
index 0000000..a6de9d2
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd
@@ -0,0 +1,42 @@
+
+
+
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diff --git a/scientific-skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd b/scientific-skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd
new file mode 100644
index 0000000..10e978b
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd
@@ -0,0 +1,50 @@
+
+
+
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diff --git a/scientific-skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd b/scientific-skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd
new file mode 100644
index 0000000..4248bf7
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd
@@ -0,0 +1,49 @@
+
+
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+
diff --git a/scientific-skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd b/scientific-skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd
new file mode 100644
index 0000000..5649746
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd
@@ -0,0 +1,33 @@
+
+
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+
diff --git a/scientific-skills/document-skills/pptx/ooxml/schemas/mce/mc.xsd b/scientific-skills/document-skills/pptx/ooxml/schemas/mce/mc.xsd
new file mode 100644
index 0000000..ef72545
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/schemas/mce/mc.xsd
@@ -0,0 +1,75 @@
+
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diff --git a/scientific-skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2010.xsd b/scientific-skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2010.xsd
new file mode 100644
index 0000000..f65f777
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2010.xsd
@@ -0,0 +1,560 @@
+
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diff --git a/scientific-skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2012.xsd b/scientific-skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2012.xsd
new file mode 100644
index 0000000..6b00755
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2012.xsd
@@ -0,0 +1,67 @@
+
+
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diff --git a/scientific-skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2018.xsd b/scientific-skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2018.xsd
new file mode 100644
index 0000000..f321d33
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2018.xsd
@@ -0,0 +1,14 @@
+
+
+
+
+
+
+
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+
+
+
+
+
diff --git a/scientific-skills/document-skills/pptx/ooxml/schemas/microsoft/wml-cex-2018.xsd b/scientific-skills/document-skills/pptx/ooxml/schemas/microsoft/wml-cex-2018.xsd
new file mode 100644
index 0000000..364c6a9
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/schemas/microsoft/wml-cex-2018.xsd
@@ -0,0 +1,20 @@
+
+
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+
diff --git a/scientific-skills/document-skills/pptx/ooxml/schemas/microsoft/wml-cid-2016.xsd b/scientific-skills/document-skills/pptx/ooxml/schemas/microsoft/wml-cid-2016.xsd
new file mode 100644
index 0000000..fed9d15
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/schemas/microsoft/wml-cid-2016.xsd
@@ -0,0 +1,13 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/scientific-skills/document-skills/pptx/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd b/scientific-skills/document-skills/pptx/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd
new file mode 100644
index 0000000..680cf15
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd
@@ -0,0 +1,4 @@
+
+
+
+
diff --git a/scientific-skills/document-skills/pptx/ooxml/schemas/microsoft/wml-symex-2015.xsd b/scientific-skills/document-skills/pptx/ooxml/schemas/microsoft/wml-symex-2015.xsd
new file mode 100644
index 0000000..89ada90
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/schemas/microsoft/wml-symex-2015.xsd
@@ -0,0 +1,8 @@
+
+
+
+
+
+
+
+
diff --git a/scientific-skills/document-skills/pptx/ooxml/scripts/pack.py b/scientific-skills/document-skills/pptx/ooxml/scripts/pack.py
new file mode 100755
index 0000000..68bc088
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/scripts/pack.py
@@ -0,0 +1,159 @@
+#!/usr/bin/env python3
+"""
+Tool to pack a directory into a .docx, .pptx, or .xlsx file with XML formatting undone.
+
+Example usage:
+ python pack.py [--force]
+"""
+
+import argparse
+import shutil
+import subprocess
+import sys
+import tempfile
+import defusedxml.minidom
+import zipfile
+from pathlib import Path
+
+
+def main():
+ parser = argparse.ArgumentParser(description="Pack a directory into an Office file")
+ parser.add_argument("input_directory", help="Unpacked Office document directory")
+ parser.add_argument("output_file", help="Output Office file (.docx/.pptx/.xlsx)")
+ parser.add_argument("--force", action="store_true", help="Skip validation")
+ args = parser.parse_args()
+
+ try:
+ success = pack_document(
+ args.input_directory, args.output_file, validate=not args.force
+ )
+
+ # Show warning if validation was skipped
+ if args.force:
+ print("Warning: Skipped validation, file may be corrupt", file=sys.stderr)
+ # Exit with error if validation failed
+ elif not success:
+ print("Contents would produce a corrupt file.", file=sys.stderr)
+ print("Please validate XML before repacking.", file=sys.stderr)
+ print("Use --force to skip validation and pack anyway.", file=sys.stderr)
+ sys.exit(1)
+
+ except ValueError as e:
+ sys.exit(f"Error: {e}")
+
+
+def pack_document(input_dir, output_file, validate=False):
+ """Pack a directory into an Office file (.docx/.pptx/.xlsx).
+
+ Args:
+ input_dir: Path to unpacked Office document directory
+ output_file: Path to output Office file
+ validate: If True, validates with soffice (default: False)
+
+ Returns:
+ bool: True if successful, False if validation failed
+ """
+ input_dir = Path(input_dir)
+ output_file = Path(output_file)
+
+ if not input_dir.is_dir():
+ raise ValueError(f"{input_dir} is not a directory")
+ if output_file.suffix.lower() not in {".docx", ".pptx", ".xlsx"}:
+ raise ValueError(f"{output_file} must be a .docx, .pptx, or .xlsx file")
+
+ # Work in temporary directory to avoid modifying original
+ with tempfile.TemporaryDirectory() as temp_dir:
+ temp_content_dir = Path(temp_dir) / "content"
+ shutil.copytree(input_dir, temp_content_dir)
+
+ # Process XML files to remove pretty-printing whitespace
+ for pattern in ["*.xml", "*.rels"]:
+ for xml_file in temp_content_dir.rglob(pattern):
+ condense_xml(xml_file)
+
+ # Create final Office file as zip archive
+ output_file.parent.mkdir(parents=True, exist_ok=True)
+ with zipfile.ZipFile(output_file, "w", zipfile.ZIP_DEFLATED) as zf:
+ for f in temp_content_dir.rglob("*"):
+ if f.is_file():
+ zf.write(f, f.relative_to(temp_content_dir))
+
+ # Validate if requested
+ if validate:
+ if not validate_document(output_file):
+ output_file.unlink() # Delete the corrupt file
+ return False
+
+ return True
+
+
+def validate_document(doc_path):
+ """Validate document by converting to HTML with soffice."""
+ # Determine the correct filter based on file extension
+ match doc_path.suffix.lower():
+ case ".docx":
+ filter_name = "html:HTML"
+ case ".pptx":
+ filter_name = "html:impress_html_Export"
+ case ".xlsx":
+ filter_name = "html:HTML (StarCalc)"
+
+ with tempfile.TemporaryDirectory() as temp_dir:
+ try:
+ result = subprocess.run(
+ [
+ "soffice",
+ "--headless",
+ "--convert-to",
+ filter_name,
+ "--outdir",
+ temp_dir,
+ str(doc_path),
+ ],
+ capture_output=True,
+ timeout=10,
+ text=True,
+ )
+ if not (Path(temp_dir) / f"{doc_path.stem}.html").exists():
+ error_msg = result.stderr.strip() or "Document validation failed"
+ print(f"Validation error: {error_msg}", file=sys.stderr)
+ return False
+ return True
+ except FileNotFoundError:
+ print("Warning: soffice not found. Skipping validation.", file=sys.stderr)
+ return True
+ except subprocess.TimeoutExpired:
+ print("Validation error: Timeout during conversion", file=sys.stderr)
+ return False
+ except Exception as e:
+ print(f"Validation error: {e}", file=sys.stderr)
+ return False
+
+
+def condense_xml(xml_file):
+ """Strip unnecessary whitespace and remove comments."""
+ with open(xml_file, "r", encoding="utf-8") as f:
+ dom = defusedxml.minidom.parse(f)
+
+ # Process each element to remove whitespace and comments
+ for element in dom.getElementsByTagName("*"):
+ # Skip w:t elements and their processing
+ if element.tagName.endswith(":t"):
+ continue
+
+ # Remove whitespace-only text nodes and comment nodes
+ for child in list(element.childNodes):
+ if (
+ child.nodeType == child.TEXT_NODE
+ and child.nodeValue
+ and child.nodeValue.strip() == ""
+ ) or child.nodeType == child.COMMENT_NODE:
+ element.removeChild(child)
+
+ # Write back the condensed XML
+ with open(xml_file, "wb") as f:
+ f.write(dom.toxml(encoding="UTF-8"))
+
+
+if __name__ == "__main__":
+ main()
diff --git a/scientific-skills/document-skills/pptx/ooxml/scripts/unpack.py b/scientific-skills/document-skills/pptx/ooxml/scripts/unpack.py
new file mode 100755
index 0000000..4938798
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/scripts/unpack.py
@@ -0,0 +1,29 @@
+#!/usr/bin/env python3
+"""Unpack and format XML contents of Office files (.docx, .pptx, .xlsx)"""
+
+import random
+import sys
+import defusedxml.minidom
+import zipfile
+from pathlib import Path
+
+# Get command line arguments
+assert len(sys.argv) == 3, "Usage: python unpack.py "
+input_file, output_dir = sys.argv[1], sys.argv[2]
+
+# Extract and format
+output_path = Path(output_dir)
+output_path.mkdir(parents=True, exist_ok=True)
+zipfile.ZipFile(input_file).extractall(output_path)
+
+# Pretty print all XML files
+xml_files = list(output_path.rglob("*.xml")) + list(output_path.rglob("*.rels"))
+for xml_file in xml_files:
+ content = xml_file.read_text(encoding="utf-8")
+ dom = defusedxml.minidom.parseString(content)
+ xml_file.write_bytes(dom.toprettyxml(indent=" ", encoding="ascii"))
+
+# For .docx files, suggest an RSID for tracked changes
+if input_file.endswith(".docx"):
+ suggested_rsid = "".join(random.choices("0123456789ABCDEF", k=8))
+ print(f"Suggested RSID for edit session: {suggested_rsid}")
diff --git a/scientific-skills/document-skills/pptx/ooxml/scripts/validate.py b/scientific-skills/document-skills/pptx/ooxml/scripts/validate.py
new file mode 100755
index 0000000..508c589
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/scripts/validate.py
@@ -0,0 +1,69 @@
+#!/usr/bin/env python3
+"""
+Command line tool to validate Office document XML files against XSD schemas and tracked changes.
+
+Usage:
+ python validate.py --original
+"""
+
+import argparse
+import sys
+from pathlib import Path
+
+from validation import DOCXSchemaValidator, PPTXSchemaValidator, RedliningValidator
+
+
+def main():
+ parser = argparse.ArgumentParser(description="Validate Office document XML files")
+ parser.add_argument(
+ "unpacked_dir",
+ help="Path to unpacked Office document directory",
+ )
+ parser.add_argument(
+ "--original",
+ required=True,
+ help="Path to original file (.docx/.pptx/.xlsx)",
+ )
+ parser.add_argument(
+ "-v",
+ "--verbose",
+ action="store_true",
+ help="Enable verbose output",
+ )
+ args = parser.parse_args()
+
+ # Validate paths
+ unpacked_dir = Path(args.unpacked_dir)
+ original_file = Path(args.original)
+ file_extension = original_file.suffix.lower()
+ assert unpacked_dir.is_dir(), f"Error: {unpacked_dir} is not a directory"
+ assert original_file.is_file(), f"Error: {original_file} is not a file"
+ assert file_extension in [".docx", ".pptx", ".xlsx"], (
+ f"Error: {original_file} must be a .docx, .pptx, or .xlsx file"
+ )
+
+ # Run validations
+ match file_extension:
+ case ".docx":
+ validators = [DOCXSchemaValidator, RedliningValidator]
+ case ".pptx":
+ validators = [PPTXSchemaValidator]
+ case _:
+ print(f"Error: Validation not supported for file type {file_extension}")
+ sys.exit(1)
+
+ # Run validators
+ success = True
+ for V in validators:
+ validator = V(unpacked_dir, original_file, verbose=args.verbose)
+ if not validator.validate():
+ success = False
+
+ if success:
+ print("All validations PASSED!")
+
+ sys.exit(0 if success else 1)
+
+
+if __name__ == "__main__":
+ main()
diff --git a/scientific-skills/document-skills/pptx/ooxml/scripts/validation/__init__.py b/scientific-skills/document-skills/pptx/ooxml/scripts/validation/__init__.py
new file mode 100644
index 0000000..db092ec
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/scripts/validation/__init__.py
@@ -0,0 +1,15 @@
+"""
+Validation modules for Word document processing.
+"""
+
+from .base import BaseSchemaValidator
+from .docx import DOCXSchemaValidator
+from .pptx import PPTXSchemaValidator
+from .redlining import RedliningValidator
+
+__all__ = [
+ "BaseSchemaValidator",
+ "DOCXSchemaValidator",
+ "PPTXSchemaValidator",
+ "RedliningValidator",
+]
diff --git a/scientific-skills/document-skills/pptx/ooxml/scripts/validation/base.py b/scientific-skills/document-skills/pptx/ooxml/scripts/validation/base.py
new file mode 100644
index 0000000..0681b19
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/scripts/validation/base.py
@@ -0,0 +1,951 @@
+"""
+Base validator with common validation logic for document files.
+"""
+
+import re
+from pathlib import Path
+
+import lxml.etree
+
+
+class BaseSchemaValidator:
+ """Base validator with common validation logic for document files."""
+
+ # Elements whose 'id' attributes must be unique within their file
+ # Format: element_name -> (attribute_name, scope)
+ # scope can be 'file' (unique within file) or 'global' (unique across all files)
+ UNIQUE_ID_REQUIREMENTS = {
+ # Word elements
+ "comment": ("id", "file"), # Comment IDs in comments.xml
+ "commentrangestart": ("id", "file"), # Must match comment IDs
+ "commentrangeend": ("id", "file"), # Must match comment IDs
+ "bookmarkstart": ("id", "file"), # Bookmark start IDs
+ "bookmarkend": ("id", "file"), # Bookmark end IDs
+ # Note: ins and del (track changes) can share IDs when part of same revision
+ # PowerPoint elements
+ "sldid": ("id", "file"), # Slide IDs in presentation.xml
+ "sldmasterid": ("id", "global"), # Slide master IDs must be globally unique
+ "sldlayoutid": ("id", "global"), # Slide layout IDs must be globally unique
+ "cm": ("authorid", "file"), # Comment author IDs
+ # Excel elements
+ "sheet": ("sheetid", "file"), # Sheet IDs in workbook.xml
+ "definedname": ("id", "file"), # Named range IDs
+ # Drawing/Shape elements (all formats)
+ "cxnsp": ("id", "file"), # Connection shape IDs
+ "sp": ("id", "file"), # Shape IDs
+ "pic": ("id", "file"), # Picture IDs
+ "grpsp": ("id", "file"), # Group shape IDs
+ }
+
+ # Mapping of element names to expected relationship types
+ # Subclasses should override this with format-specific mappings
+ ELEMENT_RELATIONSHIP_TYPES = {}
+
+ # Unified schema mappings for all Office document types
+ SCHEMA_MAPPINGS = {
+ # Document type specific schemas
+ "word": "ISO-IEC29500-4_2016/wml.xsd", # Word documents
+ "ppt": "ISO-IEC29500-4_2016/pml.xsd", # PowerPoint presentations
+ "xl": "ISO-IEC29500-4_2016/sml.xsd", # Excel spreadsheets
+ # Common file types
+ "[Content_Types].xml": "ecma/fouth-edition/opc-contentTypes.xsd",
+ "app.xml": "ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd",
+ "core.xml": "ecma/fouth-edition/opc-coreProperties.xsd",
+ "custom.xml": "ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd",
+ ".rels": "ecma/fouth-edition/opc-relationships.xsd",
+ # Word-specific files
+ "people.xml": "microsoft/wml-2012.xsd",
+ "commentsIds.xml": "microsoft/wml-cid-2016.xsd",
+ "commentsExtensible.xml": "microsoft/wml-cex-2018.xsd",
+ "commentsExtended.xml": "microsoft/wml-2012.xsd",
+ # Chart files (common across document types)
+ "chart": "ISO-IEC29500-4_2016/dml-chart.xsd",
+ # Theme files (common across document types)
+ "theme": "ISO-IEC29500-4_2016/dml-main.xsd",
+ # Drawing and media files
+ "drawing": "ISO-IEC29500-4_2016/dml-main.xsd",
+ }
+
+ # Unified namespace constants
+ MC_NAMESPACE = "http://schemas.openxmlformats.org/markup-compatibility/2006"
+ XML_NAMESPACE = "http://www.w3.org/XML/1998/namespace"
+
+ # Common OOXML namespaces used across validators
+ PACKAGE_RELATIONSHIPS_NAMESPACE = (
+ "http://schemas.openxmlformats.org/package/2006/relationships"
+ )
+ OFFICE_RELATIONSHIPS_NAMESPACE = (
+ "http://schemas.openxmlformats.org/officeDocument/2006/relationships"
+ )
+ CONTENT_TYPES_NAMESPACE = (
+ "http://schemas.openxmlformats.org/package/2006/content-types"
+ )
+
+ # Folders where we should clean ignorable namespaces
+ MAIN_CONTENT_FOLDERS = {"word", "ppt", "xl"}
+
+ # All allowed OOXML namespaces (superset of all document types)
+ OOXML_NAMESPACES = {
+ "http://schemas.openxmlformats.org/officeDocument/2006/math",
+ "http://schemas.openxmlformats.org/officeDocument/2006/relationships",
+ "http://schemas.openxmlformats.org/schemaLibrary/2006/main",
+ "http://schemas.openxmlformats.org/drawingml/2006/main",
+ "http://schemas.openxmlformats.org/drawingml/2006/chart",
+ "http://schemas.openxmlformats.org/drawingml/2006/chartDrawing",
+ "http://schemas.openxmlformats.org/drawingml/2006/diagram",
+ "http://schemas.openxmlformats.org/drawingml/2006/picture",
+ "http://schemas.openxmlformats.org/drawingml/2006/spreadsheetDrawing",
+ "http://schemas.openxmlformats.org/drawingml/2006/wordprocessingDrawing",
+ "http://schemas.openxmlformats.org/wordprocessingml/2006/main",
+ "http://schemas.openxmlformats.org/presentationml/2006/main",
+ "http://schemas.openxmlformats.org/spreadsheetml/2006/main",
+ "http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes",
+ "http://www.w3.org/XML/1998/namespace",
+ }
+
+ def __init__(self, unpacked_dir, original_file, verbose=False):
+ self.unpacked_dir = Path(unpacked_dir).resolve()
+ self.original_file = Path(original_file)
+ self.verbose = verbose
+
+ # Set schemas directory
+ self.schemas_dir = Path(__file__).parent.parent.parent / "schemas"
+
+ # Get all XML and .rels files
+ patterns = ["*.xml", "*.rels"]
+ self.xml_files = [
+ f for pattern in patterns for f in self.unpacked_dir.rglob(pattern)
+ ]
+
+ if not self.xml_files:
+ print(f"Warning: No XML files found in {self.unpacked_dir}")
+
+ def validate(self):
+ """Run all validation checks and return True if all pass."""
+ raise NotImplementedError("Subclasses must implement the validate method")
+
+ def validate_xml(self):
+ """Validate that all XML files are well-formed."""
+ errors = []
+
+ for xml_file in self.xml_files:
+ try:
+ # Try to parse the XML file
+ lxml.etree.parse(str(xml_file))
+ except lxml.etree.XMLSyntaxError as e:
+ errors.append(
+ f" {xml_file.relative_to(self.unpacked_dir)}: "
+ f"Line {e.lineno}: {e.msg}"
+ )
+ except Exception as e:
+ errors.append(
+ f" {xml_file.relative_to(self.unpacked_dir)}: "
+ f"Unexpected error: {str(e)}"
+ )
+
+ if errors:
+ print(f"FAILED - Found {len(errors)} XML violations:")
+ for error in errors:
+ print(error)
+ return False
+ else:
+ if self.verbose:
+ print("PASSED - All XML files are well-formed")
+ return True
+
+ def validate_namespaces(self):
+ """Validate that namespace prefixes in Ignorable attributes are declared."""
+ errors = []
+
+ for xml_file in self.xml_files:
+ try:
+ root = lxml.etree.parse(str(xml_file)).getroot()
+ declared = set(root.nsmap.keys()) - {None} # Exclude default namespace
+
+ for attr_val in [
+ v for k, v in root.attrib.items() if k.endswith("Ignorable")
+ ]:
+ undeclared = set(attr_val.split()) - declared
+ errors.extend(
+ f" {xml_file.relative_to(self.unpacked_dir)}: "
+ f"Namespace '{ns}' in Ignorable but not declared"
+ for ns in undeclared
+ )
+ except lxml.etree.XMLSyntaxError:
+ continue
+
+ if errors:
+ print(f"FAILED - {len(errors)} namespace issues:")
+ for error in errors:
+ print(error)
+ return False
+ if self.verbose:
+ print("PASSED - All namespace prefixes properly declared")
+ return True
+
+ def validate_unique_ids(self):
+ """Validate that specific IDs are unique according to OOXML requirements."""
+ errors = []
+ global_ids = {} # Track globally unique IDs across all files
+
+ for xml_file in self.xml_files:
+ try:
+ root = lxml.etree.parse(str(xml_file)).getroot()
+ file_ids = {} # Track IDs that must be unique within this file
+
+ # Remove all mc:AlternateContent elements from the tree
+ mc_elements = root.xpath(
+ ".//mc:AlternateContent", namespaces={"mc": self.MC_NAMESPACE}
+ )
+ for elem in mc_elements:
+ elem.getparent().remove(elem)
+
+ # Now check IDs in the cleaned tree
+ for elem in root.iter():
+ # Get the element name without namespace
+ tag = (
+ elem.tag.split("}")[-1].lower()
+ if "}" in elem.tag
+ else elem.tag.lower()
+ )
+
+ # Check if this element type has ID uniqueness requirements
+ if tag in self.UNIQUE_ID_REQUIREMENTS:
+ attr_name, scope = self.UNIQUE_ID_REQUIREMENTS[tag]
+
+ # Look for the specified attribute
+ id_value = None
+ for attr, value in elem.attrib.items():
+ attr_local = (
+ attr.split("}")[-1].lower()
+ if "}" in attr
+ else attr.lower()
+ )
+ if attr_local == attr_name:
+ id_value = value
+ break
+
+ if id_value is not None:
+ if scope == "global":
+ # Check global uniqueness
+ if id_value in global_ids:
+ prev_file, prev_line, prev_tag = global_ids[
+ id_value
+ ]
+ errors.append(
+ f" {xml_file.relative_to(self.unpacked_dir)}: "
+ f"Line {elem.sourceline}: Global ID '{id_value}' in <{tag}> "
+ f"already used in {prev_file} at line {prev_line} in <{prev_tag}>"
+ )
+ else:
+ global_ids[id_value] = (
+ xml_file.relative_to(self.unpacked_dir),
+ elem.sourceline,
+ tag,
+ )
+ elif scope == "file":
+ # Check file-level uniqueness
+ key = (tag, attr_name)
+ if key not in file_ids:
+ file_ids[key] = {}
+
+ if id_value in file_ids[key]:
+ prev_line = file_ids[key][id_value]
+ errors.append(
+ f" {xml_file.relative_to(self.unpacked_dir)}: "
+ f"Line {elem.sourceline}: Duplicate {attr_name}='{id_value}' in <{tag}> "
+ f"(first occurrence at line {prev_line})"
+ )
+ else:
+ file_ids[key][id_value] = elem.sourceline
+
+ except (lxml.etree.XMLSyntaxError, Exception) as e:
+ errors.append(
+ f" {xml_file.relative_to(self.unpacked_dir)}: Error: {e}"
+ )
+
+ if errors:
+ print(f"FAILED - Found {len(errors)} ID uniqueness violations:")
+ for error in errors:
+ print(error)
+ return False
+ else:
+ if self.verbose:
+ print("PASSED - All required IDs are unique")
+ return True
+
+ def validate_file_references(self):
+ """
+ Validate that all .rels files properly reference files and that all files are referenced.
+ """
+ errors = []
+
+ # Find all .rels files
+ rels_files = list(self.unpacked_dir.rglob("*.rels"))
+
+ if not rels_files:
+ if self.verbose:
+ print("PASSED - No .rels files found")
+ return True
+
+ # Get all files in the unpacked directory (excluding reference files)
+ all_files = []
+ for file_path in self.unpacked_dir.rglob("*"):
+ if (
+ file_path.is_file()
+ and file_path.name != "[Content_Types].xml"
+ and not file_path.name.endswith(".rels")
+ ): # This file is not referenced by .rels
+ all_files.append(file_path.resolve())
+
+ # Track all files that are referenced by any .rels file
+ all_referenced_files = set()
+
+ if self.verbose:
+ print(
+ f"Found {len(rels_files)} .rels files and {len(all_files)} target files"
+ )
+
+ # Check each .rels file
+ for rels_file in rels_files:
+ try:
+ # Parse relationships file
+ rels_root = lxml.etree.parse(str(rels_file)).getroot()
+
+ # Get the directory where this .rels file is located
+ rels_dir = rels_file.parent
+
+ # Find all relationships and their targets
+ referenced_files = set()
+ broken_refs = []
+
+ for rel in rels_root.findall(
+ ".//ns:Relationship",
+ namespaces={"ns": self.PACKAGE_RELATIONSHIPS_NAMESPACE},
+ ):
+ target = rel.get("Target")
+ if target and not target.startswith(
+ ("http", "mailto:")
+ ): # Skip external URLs
+ # Resolve the target path relative to the .rels file location
+ if rels_file.name == ".rels":
+ # Root .rels file - targets are relative to unpacked_dir
+ target_path = self.unpacked_dir / target
+ else:
+ # Other .rels files - targets are relative to their parent's parent
+ # e.g., word/_rels/document.xml.rels -> targets relative to word/
+ base_dir = rels_dir.parent
+ target_path = base_dir / target
+
+ # Normalize the path and check if it exists
+ try:
+ target_path = target_path.resolve()
+ if target_path.exists() and target_path.is_file():
+ referenced_files.add(target_path)
+ all_referenced_files.add(target_path)
+ else:
+ broken_refs.append((target, rel.sourceline))
+ except (OSError, ValueError):
+ broken_refs.append((target, rel.sourceline))
+
+ # Report broken references
+ if broken_refs:
+ rel_path = rels_file.relative_to(self.unpacked_dir)
+ for broken_ref, line_num in broken_refs:
+ errors.append(
+ f" {rel_path}: Line {line_num}: Broken reference to {broken_ref}"
+ )
+
+ except Exception as e:
+ rel_path = rels_file.relative_to(self.unpacked_dir)
+ errors.append(f" Error parsing {rel_path}: {e}")
+
+ # Check for unreferenced files (files that exist but are not referenced anywhere)
+ unreferenced_files = set(all_files) - all_referenced_files
+
+ if unreferenced_files:
+ for unref_file in sorted(unreferenced_files):
+ unref_rel_path = unref_file.relative_to(self.unpacked_dir)
+ errors.append(f" Unreferenced file: {unref_rel_path}")
+
+ if errors:
+ print(f"FAILED - Found {len(errors)} relationship validation errors:")
+ for error in errors:
+ print(error)
+ print(
+ "CRITICAL: These errors will cause the document to appear corrupt. "
+ + "Broken references MUST be fixed, "
+ + "and unreferenced files MUST be referenced or removed."
+ )
+ return False
+ else:
+ if self.verbose:
+ print(
+ "PASSED - All references are valid and all files are properly referenced"
+ )
+ return True
+
+ def validate_all_relationship_ids(self):
+ """
+ Validate that all r:id attributes in XML files reference existing IDs
+ in their corresponding .rels files, and optionally validate relationship types.
+ """
+ import lxml.etree
+
+ errors = []
+
+ # Process each XML file that might contain r:id references
+ for xml_file in self.xml_files:
+ # Skip .rels files themselves
+ if xml_file.suffix == ".rels":
+ continue
+
+ # Determine the corresponding .rels file
+ # For dir/file.xml, it's dir/_rels/file.xml.rels
+ rels_dir = xml_file.parent / "_rels"
+ rels_file = rels_dir / f"{xml_file.name}.rels"
+
+ # Skip if there's no corresponding .rels file (that's okay)
+ if not rels_file.exists():
+ continue
+
+ try:
+ # Parse the .rels file to get valid relationship IDs and their types
+ rels_root = lxml.etree.parse(str(rels_file)).getroot()
+ rid_to_type = {}
+
+ for rel in rels_root.findall(
+ f".//{{{self.PACKAGE_RELATIONSHIPS_NAMESPACE}}}Relationship"
+ ):
+ rid = rel.get("Id")
+ rel_type = rel.get("Type", "")
+ if rid:
+ # Check for duplicate rIds
+ if rid in rid_to_type:
+ rels_rel_path = rels_file.relative_to(self.unpacked_dir)
+ errors.append(
+ f" {rels_rel_path}: Line {rel.sourceline}: "
+ f"Duplicate relationship ID '{rid}' (IDs must be unique)"
+ )
+ # Extract just the type name from the full URL
+ type_name = (
+ rel_type.split("/")[-1] if "/" in rel_type else rel_type
+ )
+ rid_to_type[rid] = type_name
+
+ # Parse the XML file to find all r:id references
+ xml_root = lxml.etree.parse(str(xml_file)).getroot()
+
+ # Find all elements with r:id attributes
+ for elem in xml_root.iter():
+ # Check for r:id attribute (relationship ID)
+ rid_attr = elem.get(f"{{{self.OFFICE_RELATIONSHIPS_NAMESPACE}}}id")
+ if rid_attr:
+ xml_rel_path = xml_file.relative_to(self.unpacked_dir)
+ elem_name = (
+ elem.tag.split("}")[-1] if "}" in elem.tag else elem.tag
+ )
+
+ # Check if the ID exists
+ if rid_attr not in rid_to_type:
+ errors.append(
+ f" {xml_rel_path}: Line {elem.sourceline}: "
+ f"<{elem_name}> references non-existent relationship '{rid_attr}' "
+ f"(valid IDs: {', '.join(sorted(rid_to_type.keys())[:5])}{'...' if len(rid_to_type) > 5 else ''})"
+ )
+ # Check if we have type expectations for this element
+ elif self.ELEMENT_RELATIONSHIP_TYPES:
+ expected_type = self._get_expected_relationship_type(
+ elem_name
+ )
+ if expected_type:
+ actual_type = rid_to_type[rid_attr]
+ # Check if the actual type matches or contains the expected type
+ if expected_type not in actual_type.lower():
+ errors.append(
+ f" {xml_rel_path}: Line {elem.sourceline}: "
+ f"<{elem_name}> references '{rid_attr}' which points to '{actual_type}' "
+ f"but should point to a '{expected_type}' relationship"
+ )
+
+ except Exception as e:
+ xml_rel_path = xml_file.relative_to(self.unpacked_dir)
+ errors.append(f" Error processing {xml_rel_path}: {e}")
+
+ if errors:
+ print(f"FAILED - Found {len(errors)} relationship ID reference errors:")
+ for error in errors:
+ print(error)
+ print("\nThese ID mismatches will cause the document to appear corrupt!")
+ return False
+ else:
+ if self.verbose:
+ print("PASSED - All relationship ID references are valid")
+ return True
+
+ def _get_expected_relationship_type(self, element_name):
+ """
+ Get the expected relationship type for an element.
+ First checks the explicit mapping, then tries pattern detection.
+ """
+ # Normalize element name to lowercase
+ elem_lower = element_name.lower()
+
+ # Check explicit mapping first
+ if elem_lower in self.ELEMENT_RELATIONSHIP_TYPES:
+ return self.ELEMENT_RELATIONSHIP_TYPES[elem_lower]
+
+ # Try pattern detection for common patterns
+ # Pattern 1: Elements ending in "Id" often expect a relationship of the prefix type
+ if elem_lower.endswith("id") and len(elem_lower) > 2:
+ # e.g., "sldId" -> "sld", "sldMasterId" -> "sldMaster"
+ prefix = elem_lower[:-2] # Remove "id"
+ # Check if this might be a compound like "sldMasterId"
+ if prefix.endswith("master"):
+ return prefix.lower()
+ elif prefix.endswith("layout"):
+ return prefix.lower()
+ else:
+ # Simple case like "sldId" -> "slide"
+ # Common transformations
+ if prefix == "sld":
+ return "slide"
+ return prefix.lower()
+
+ # Pattern 2: Elements ending in "Reference" expect a relationship of the prefix type
+ if elem_lower.endswith("reference") and len(elem_lower) > 9:
+ prefix = elem_lower[:-9] # Remove "reference"
+ return prefix.lower()
+
+ return None
+
+ def validate_content_types(self):
+ """Validate that all content files are properly declared in [Content_Types].xml."""
+ errors = []
+
+ # Find [Content_Types].xml file
+ content_types_file = self.unpacked_dir / "[Content_Types].xml"
+ if not content_types_file.exists():
+ print("FAILED - [Content_Types].xml file not found")
+ return False
+
+ try:
+ # Parse and get all declared parts and extensions
+ root = lxml.etree.parse(str(content_types_file)).getroot()
+ declared_parts = set()
+ declared_extensions = set()
+
+ # Get Override declarations (specific files)
+ for override in root.findall(
+ f".//{{{self.CONTENT_TYPES_NAMESPACE}}}Override"
+ ):
+ part_name = override.get("PartName")
+ if part_name is not None:
+ declared_parts.add(part_name.lstrip("/"))
+
+ # Get Default declarations (by extension)
+ for default in root.findall(
+ f".//{{{self.CONTENT_TYPES_NAMESPACE}}}Default"
+ ):
+ extension = default.get("Extension")
+ if extension is not None:
+ declared_extensions.add(extension.lower())
+
+ # Root elements that require content type declaration
+ declarable_roots = {
+ "sld",
+ "sldLayout",
+ "sldMaster",
+ "presentation", # PowerPoint
+ "document", # Word
+ "workbook",
+ "worksheet", # Excel
+ "theme", # Common
+ }
+
+ # Common media file extensions that should be declared
+ media_extensions = {
+ "png": "image/png",
+ "jpg": "image/jpeg",
+ "jpeg": "image/jpeg",
+ "gif": "image/gif",
+ "bmp": "image/bmp",
+ "tiff": "image/tiff",
+ "wmf": "image/x-wmf",
+ "emf": "image/x-emf",
+ }
+
+ # Get all files in the unpacked directory
+ all_files = list(self.unpacked_dir.rglob("*"))
+ all_files = [f for f in all_files if f.is_file()]
+
+ # Check all XML files for Override declarations
+ for xml_file in self.xml_files:
+ path_str = str(xml_file.relative_to(self.unpacked_dir)).replace(
+ "\\", "/"
+ )
+
+ # Skip non-content files
+ if any(
+ skip in path_str
+ for skip in [".rels", "[Content_Types]", "docProps/", "_rels/"]
+ ):
+ continue
+
+ try:
+ root_tag = lxml.etree.parse(str(xml_file)).getroot().tag
+ root_name = root_tag.split("}")[-1] if "}" in root_tag else root_tag
+
+ if root_name in declarable_roots and path_str not in declared_parts:
+ errors.append(
+ f" {path_str}: File with <{root_name}> root not declared in [Content_Types].xml"
+ )
+
+ except Exception:
+ continue # Skip unparseable files
+
+ # Check all non-XML files for Default extension declarations
+ for file_path in all_files:
+ # Skip XML files and metadata files (already checked above)
+ if file_path.suffix.lower() in {".xml", ".rels"}:
+ continue
+ if file_path.name == "[Content_Types].xml":
+ continue
+ if "_rels" in file_path.parts or "docProps" in file_path.parts:
+ continue
+
+ extension = file_path.suffix.lstrip(".").lower()
+ if extension and extension not in declared_extensions:
+ # Check if it's a known media extension that should be declared
+ if extension in media_extensions:
+ relative_path = file_path.relative_to(self.unpacked_dir)
+ errors.append(
+ f' {relative_path}: File with extension \'{extension}\' not declared in [Content_Types].xml - should add: '
+ )
+
+ except Exception as e:
+ errors.append(f" Error parsing [Content_Types].xml: {e}")
+
+ if errors:
+ print(f"FAILED - Found {len(errors)} content type declaration errors:")
+ for error in errors:
+ print(error)
+ return False
+ else:
+ if self.verbose:
+ print(
+ "PASSED - All content files are properly declared in [Content_Types].xml"
+ )
+ return True
+
+ def validate_file_against_xsd(self, xml_file, verbose=False):
+ """Validate a single XML file against XSD schema, comparing with original.
+
+ Args:
+ xml_file: Path to XML file to validate
+ verbose: Enable verbose output
+
+ Returns:
+ tuple: (is_valid, new_errors_set) where is_valid is True/False/None (skipped)
+ """
+ # Resolve both paths to handle symlinks
+ xml_file = Path(xml_file).resolve()
+ unpacked_dir = self.unpacked_dir.resolve()
+
+ # Validate current file
+ is_valid, current_errors = self._validate_single_file_xsd(
+ xml_file, unpacked_dir
+ )
+
+ if is_valid is None:
+ return None, set() # Skipped
+ elif is_valid:
+ return True, set() # Valid, no errors
+
+ # Get errors from original file for this specific file
+ original_errors = self._get_original_file_errors(xml_file)
+
+ # Compare with original (both are guaranteed to be sets here)
+ assert current_errors is not None
+ new_errors = current_errors - original_errors
+
+ if new_errors:
+ if verbose:
+ relative_path = xml_file.relative_to(unpacked_dir)
+ print(f"FAILED - {relative_path}: {len(new_errors)} new error(s)")
+ for error in list(new_errors)[:3]:
+ truncated = error[:250] + "..." if len(error) > 250 else error
+ print(f" - {truncated}")
+ return False, new_errors
+ else:
+ # All errors existed in original
+ if verbose:
+ print(
+ f"PASSED - No new errors (original had {len(current_errors)} errors)"
+ )
+ return True, set()
+
+ def validate_against_xsd(self):
+ """Validate XML files against XSD schemas, showing only new errors compared to original."""
+ new_errors = []
+ original_error_count = 0
+ valid_count = 0
+ skipped_count = 0
+
+ for xml_file in self.xml_files:
+ relative_path = str(xml_file.relative_to(self.unpacked_dir))
+ is_valid, new_file_errors = self.validate_file_against_xsd(
+ xml_file, verbose=False
+ )
+
+ if is_valid is None:
+ skipped_count += 1
+ continue
+ elif is_valid and not new_file_errors:
+ valid_count += 1
+ continue
+ elif is_valid:
+ # Had errors but all existed in original
+ original_error_count += 1
+ valid_count += 1
+ continue
+
+ # Has new errors
+ new_errors.append(f" {relative_path}: {len(new_file_errors)} new error(s)")
+ for error in list(new_file_errors)[:3]: # Show first 3 errors
+ new_errors.append(
+ f" - {error[:250]}..." if len(error) > 250 else f" - {error}"
+ )
+
+ # Print summary
+ if self.verbose:
+ print(f"Validated {len(self.xml_files)} files:")
+ print(f" - Valid: {valid_count}")
+ print(f" - Skipped (no schema): {skipped_count}")
+ if original_error_count:
+ print(f" - With original errors (ignored): {original_error_count}")
+ print(
+ f" - With NEW errors: {len(new_errors) > 0 and len([e for e in new_errors if not e.startswith(' ')]) or 0}"
+ )
+
+ if new_errors:
+ print("\nFAILED - Found NEW validation errors:")
+ for error in new_errors:
+ print(error)
+ return False
+ else:
+ if self.verbose:
+ print("\nPASSED - No new XSD validation errors introduced")
+ return True
+
+ def _get_schema_path(self, xml_file):
+ """Determine the appropriate schema path for an XML file."""
+ # Check exact filename match
+ if xml_file.name in self.SCHEMA_MAPPINGS:
+ return self.schemas_dir / self.SCHEMA_MAPPINGS[xml_file.name]
+
+ # Check .rels files
+ if xml_file.suffix == ".rels":
+ return self.schemas_dir / self.SCHEMA_MAPPINGS[".rels"]
+
+ # Check chart files
+ if "charts/" in str(xml_file) and xml_file.name.startswith("chart"):
+ return self.schemas_dir / self.SCHEMA_MAPPINGS["chart"]
+
+ # Check theme files
+ if "theme/" in str(xml_file) and xml_file.name.startswith("theme"):
+ return self.schemas_dir / self.SCHEMA_MAPPINGS["theme"]
+
+ # Check if file is in a main content folder and use appropriate schema
+ if xml_file.parent.name in self.MAIN_CONTENT_FOLDERS:
+ return self.schemas_dir / self.SCHEMA_MAPPINGS[xml_file.parent.name]
+
+ return None
+
+ def _clean_ignorable_namespaces(self, xml_doc):
+ """Remove attributes and elements not in allowed namespaces."""
+ # Create a clean copy
+ xml_string = lxml.etree.tostring(xml_doc, encoding="unicode")
+ xml_copy = lxml.etree.fromstring(xml_string)
+
+ # Remove attributes not in allowed namespaces
+ for elem in xml_copy.iter():
+ attrs_to_remove = []
+
+ for attr in elem.attrib:
+ # Check if attribute is from a namespace other than allowed ones
+ if "{" in attr:
+ ns = attr.split("}")[0][1:]
+ if ns not in self.OOXML_NAMESPACES:
+ attrs_to_remove.append(attr)
+
+ # Remove collected attributes
+ for attr in attrs_to_remove:
+ del elem.attrib[attr]
+
+ # Remove elements not in allowed namespaces
+ self._remove_ignorable_elements(xml_copy)
+
+ return lxml.etree.ElementTree(xml_copy)
+
+ def _remove_ignorable_elements(self, root):
+ """Recursively remove all elements not in allowed namespaces."""
+ elements_to_remove = []
+
+ # Find elements to remove
+ for elem in list(root):
+ # Skip non-element nodes (comments, processing instructions, etc.)
+ if not hasattr(elem, "tag") or callable(elem.tag):
+ continue
+
+ tag_str = str(elem.tag)
+ if tag_str.startswith("{"):
+ ns = tag_str.split("}")[0][1:]
+ if ns not in self.OOXML_NAMESPACES:
+ elements_to_remove.append(elem)
+ continue
+
+ # Recursively clean child elements
+ self._remove_ignorable_elements(elem)
+
+ # Remove collected elements
+ for elem in elements_to_remove:
+ root.remove(elem)
+
+ def _preprocess_for_mc_ignorable(self, xml_doc):
+ """Preprocess XML to handle mc:Ignorable attribute properly."""
+ # Remove mc:Ignorable attributes before validation
+ root = xml_doc.getroot()
+
+ # Remove mc:Ignorable attribute from root
+ if f"{{{self.MC_NAMESPACE}}}Ignorable" in root.attrib:
+ del root.attrib[f"{{{self.MC_NAMESPACE}}}Ignorable"]
+
+ return xml_doc
+
+ def _validate_single_file_xsd(self, xml_file, base_path):
+ """Validate a single XML file against XSD schema. Returns (is_valid, errors_set)."""
+ schema_path = self._get_schema_path(xml_file)
+ if not schema_path:
+ return None, None # Skip file
+
+ try:
+ # Load schema
+ with open(schema_path, "rb") as xsd_file:
+ parser = lxml.etree.XMLParser()
+ xsd_doc = lxml.etree.parse(
+ xsd_file, parser=parser, base_url=str(schema_path)
+ )
+ schema = lxml.etree.XMLSchema(xsd_doc)
+
+ # Load and preprocess XML
+ with open(xml_file, "r") as f:
+ xml_doc = lxml.etree.parse(f)
+
+ xml_doc, _ = self._remove_template_tags_from_text_nodes(xml_doc)
+ xml_doc = self._preprocess_for_mc_ignorable(xml_doc)
+
+ # Clean ignorable namespaces if needed
+ relative_path = xml_file.relative_to(base_path)
+ if (
+ relative_path.parts
+ and relative_path.parts[0] in self.MAIN_CONTENT_FOLDERS
+ ):
+ xml_doc = self._clean_ignorable_namespaces(xml_doc)
+
+ # Validate
+ if schema.validate(xml_doc):
+ return True, set()
+ else:
+ errors = set()
+ for error in schema.error_log:
+ # Store normalized error message (without line numbers for comparison)
+ errors.add(error.message)
+ return False, errors
+
+ except Exception as e:
+ return False, {str(e)}
+
+ def _get_original_file_errors(self, xml_file):
+ """Get XSD validation errors from a single file in the original document.
+
+ Args:
+ xml_file: Path to the XML file in unpacked_dir to check
+
+ Returns:
+ set: Set of error messages from the original file
+ """
+ import tempfile
+ import zipfile
+
+ # Resolve both paths to handle symlinks (e.g., /var vs /private/var on macOS)
+ xml_file = Path(xml_file).resolve()
+ unpacked_dir = self.unpacked_dir.resolve()
+ relative_path = xml_file.relative_to(unpacked_dir)
+
+ with tempfile.TemporaryDirectory() as temp_dir:
+ temp_path = Path(temp_dir)
+
+ # Extract original file
+ with zipfile.ZipFile(self.original_file, "r") as zip_ref:
+ zip_ref.extractall(temp_path)
+
+ # Find corresponding file in original
+ original_xml_file = temp_path / relative_path
+
+ if not original_xml_file.exists():
+ # File didn't exist in original, so no original errors
+ return set()
+
+ # Validate the specific file in original
+ is_valid, errors = self._validate_single_file_xsd(
+ original_xml_file, temp_path
+ )
+ return errors if errors else set()
+
+ def _remove_template_tags_from_text_nodes(self, xml_doc):
+ """Remove template tags from XML text nodes and collect warnings.
+
+ Template tags follow the pattern {{ ... }} and are used as placeholders
+ for content replacement. They should be removed from text content before
+ XSD validation while preserving XML structure.
+
+ Returns:
+ tuple: (cleaned_xml_doc, warnings_list)
+ """
+ warnings = []
+ template_pattern = re.compile(r"\{\{[^}]*\}\}")
+
+ # Create a copy of the document to avoid modifying the original
+ xml_string = lxml.etree.tostring(xml_doc, encoding="unicode")
+ xml_copy = lxml.etree.fromstring(xml_string)
+
+ def process_text_content(text, content_type):
+ if not text:
+ return text
+ matches = list(template_pattern.finditer(text))
+ if matches:
+ for match in matches:
+ warnings.append(
+ f"Found template tag in {content_type}: {match.group()}"
+ )
+ return template_pattern.sub("", text)
+ return text
+
+ # Process all text nodes in the document
+ for elem in xml_copy.iter():
+ # Skip processing if this is a w:t element
+ if not hasattr(elem, "tag") or callable(elem.tag):
+ continue
+ tag_str = str(elem.tag)
+ if tag_str.endswith("}t") or tag_str == "t":
+ continue
+
+ elem.text = process_text_content(elem.text, "text content")
+ elem.tail = process_text_content(elem.tail, "tail content")
+
+ return lxml.etree.ElementTree(xml_copy), warnings
+
+
+if __name__ == "__main__":
+ raise RuntimeError("This module should not be run directly.")
diff --git a/scientific-skills/document-skills/pptx/ooxml/scripts/validation/docx.py b/scientific-skills/document-skills/pptx/ooxml/scripts/validation/docx.py
new file mode 100644
index 0000000..602c470
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/scripts/validation/docx.py
@@ -0,0 +1,274 @@
+"""
+Validator for Word document XML files against XSD schemas.
+"""
+
+import re
+import tempfile
+import zipfile
+
+import lxml.etree
+
+from .base import BaseSchemaValidator
+
+
+class DOCXSchemaValidator(BaseSchemaValidator):
+ """Validator for Word document XML files against XSD schemas."""
+
+ # Word-specific namespace
+ WORD_2006_NAMESPACE = "http://schemas.openxmlformats.org/wordprocessingml/2006/main"
+
+ # Word-specific element to relationship type mappings
+ # Start with empty mapping - add specific cases as we discover them
+ ELEMENT_RELATIONSHIP_TYPES = {}
+
+ def validate(self):
+ """Run all validation checks and return True if all pass."""
+ # Test 0: XML well-formedness
+ if not self.validate_xml():
+ return False
+
+ # Test 1: Namespace declarations
+ all_valid = True
+ if not self.validate_namespaces():
+ all_valid = False
+
+ # Test 2: Unique IDs
+ if not self.validate_unique_ids():
+ all_valid = False
+
+ # Test 3: Relationship and file reference validation
+ if not self.validate_file_references():
+ all_valid = False
+
+ # Test 4: Content type declarations
+ if not self.validate_content_types():
+ all_valid = False
+
+ # Test 5: XSD schema validation
+ if not self.validate_against_xsd():
+ all_valid = False
+
+ # Test 6: Whitespace preservation
+ if not self.validate_whitespace_preservation():
+ all_valid = False
+
+ # Test 7: Deletion validation
+ if not self.validate_deletions():
+ all_valid = False
+
+ # Test 8: Insertion validation
+ if not self.validate_insertions():
+ all_valid = False
+
+ # Test 9: Relationship ID reference validation
+ if not self.validate_all_relationship_ids():
+ all_valid = False
+
+ # Count and compare paragraphs
+ self.compare_paragraph_counts()
+
+ return all_valid
+
+ def validate_whitespace_preservation(self):
+ """
+ Validate that w:t elements with whitespace have xml:space='preserve'.
+ """
+ errors = []
+
+ for xml_file in self.xml_files:
+ # Only check document.xml files
+ if xml_file.name != "document.xml":
+ continue
+
+ try:
+ root = lxml.etree.parse(str(xml_file)).getroot()
+
+ # Find all w:t elements
+ for elem in root.iter(f"{{{self.WORD_2006_NAMESPACE}}}t"):
+ if elem.text:
+ text = elem.text
+ # Check if text starts or ends with whitespace
+ if re.match(r"^\s.*", text) or re.match(r".*\s$", text):
+ # Check if xml:space="preserve" attribute exists
+ xml_space_attr = f"{{{self.XML_NAMESPACE}}}space"
+ if (
+ xml_space_attr not in elem.attrib
+ or elem.attrib[xml_space_attr] != "preserve"
+ ):
+ # Show a preview of the text
+ text_preview = (
+ repr(text)[:50] + "..."
+ if len(repr(text)) > 50
+ else repr(text)
+ )
+ errors.append(
+ f" {xml_file.relative_to(self.unpacked_dir)}: "
+ f"Line {elem.sourceline}: w:t element with whitespace missing xml:space='preserve': {text_preview}"
+ )
+
+ except (lxml.etree.XMLSyntaxError, Exception) as e:
+ errors.append(
+ f" {xml_file.relative_to(self.unpacked_dir)}: Error: {e}"
+ )
+
+ if errors:
+ print(f"FAILED - Found {len(errors)} whitespace preservation violations:")
+ for error in errors:
+ print(error)
+ return False
+ else:
+ if self.verbose:
+ print("PASSED - All whitespace is properly preserved")
+ return True
+
+ def validate_deletions(self):
+ """
+ Validate that w:t elements are not within w:del elements.
+ For some reason, XSD validation does not catch this, so we do it manually.
+ """
+ errors = []
+
+ for xml_file in self.xml_files:
+ # Only check document.xml files
+ if xml_file.name != "document.xml":
+ continue
+
+ try:
+ root = lxml.etree.parse(str(xml_file)).getroot()
+
+ # Find all w:t elements that are descendants of w:del elements
+ namespaces = {"w": self.WORD_2006_NAMESPACE}
+ xpath_expression = ".//w:del//w:t"
+ problematic_t_elements = root.xpath(
+ xpath_expression, namespaces=namespaces
+ )
+ for t_elem in problematic_t_elements:
+ if t_elem.text:
+ # Show a preview of the text
+ text_preview = (
+ repr(t_elem.text)[:50] + "..."
+ if len(repr(t_elem.text)) > 50
+ else repr(t_elem.text)
+ )
+ errors.append(
+ f" {xml_file.relative_to(self.unpacked_dir)}: "
+ f"Line {t_elem.sourceline}: found within : {text_preview}"
+ )
+
+ except (lxml.etree.XMLSyntaxError, Exception) as e:
+ errors.append(
+ f" {xml_file.relative_to(self.unpacked_dir)}: Error: {e}"
+ )
+
+ if errors:
+ print(f"FAILED - Found {len(errors)} deletion validation violations:")
+ for error in errors:
+ print(error)
+ return False
+ else:
+ if self.verbose:
+ print("PASSED - No w:t elements found within w:del elements")
+ return True
+
+ def count_paragraphs_in_unpacked(self):
+ """Count the number of paragraphs in the unpacked document."""
+ count = 0
+
+ for xml_file in self.xml_files:
+ # Only check document.xml files
+ if xml_file.name != "document.xml":
+ continue
+
+ try:
+ root = lxml.etree.parse(str(xml_file)).getroot()
+ # Count all w:p elements
+ paragraphs = root.findall(f".//{{{self.WORD_2006_NAMESPACE}}}p")
+ count = len(paragraphs)
+ except Exception as e:
+ print(f"Error counting paragraphs in unpacked document: {e}")
+
+ return count
+
+ def count_paragraphs_in_original(self):
+ """Count the number of paragraphs in the original docx file."""
+ count = 0
+
+ try:
+ # Create temporary directory to unpack original
+ with tempfile.TemporaryDirectory() as temp_dir:
+ # Unpack original docx
+ with zipfile.ZipFile(self.original_file, "r") as zip_ref:
+ zip_ref.extractall(temp_dir)
+
+ # Parse document.xml
+ doc_xml_path = temp_dir + "/word/document.xml"
+ root = lxml.etree.parse(doc_xml_path).getroot()
+
+ # Count all w:p elements
+ paragraphs = root.findall(f".//{{{self.WORD_2006_NAMESPACE}}}p")
+ count = len(paragraphs)
+
+ except Exception as e:
+ print(f"Error counting paragraphs in original document: {e}")
+
+ return count
+
+ def validate_insertions(self):
+ """
+ Validate that w:delText elements are not within w:ins elements.
+ w:delText is only allowed in w:ins if nested within a w:del.
+ """
+ errors = []
+
+ for xml_file in self.xml_files:
+ if xml_file.name != "document.xml":
+ continue
+
+ try:
+ root = lxml.etree.parse(str(xml_file)).getroot()
+ namespaces = {"w": self.WORD_2006_NAMESPACE}
+
+ # Find w:delText in w:ins that are NOT within w:del
+ invalid_elements = root.xpath(
+ ".//w:ins//w:delText[not(ancestor::w:del)]",
+ namespaces=namespaces
+ )
+
+ for elem in invalid_elements:
+ text_preview = (
+ repr(elem.text or "")[:50] + "..."
+ if len(repr(elem.text or "")) > 50
+ else repr(elem.text or "")
+ )
+ errors.append(
+ f" {xml_file.relative_to(self.unpacked_dir)}: "
+ f"Line {elem.sourceline}: within : {text_preview}"
+ )
+
+ except (lxml.etree.XMLSyntaxError, Exception) as e:
+ errors.append(
+ f" {xml_file.relative_to(self.unpacked_dir)}: Error: {e}"
+ )
+
+ if errors:
+ print(f"FAILED - Found {len(errors)} insertion validation violations:")
+ for error in errors:
+ print(error)
+ return False
+ else:
+ if self.verbose:
+ print("PASSED - No w:delText elements within w:ins elements")
+ return True
+
+ def compare_paragraph_counts(self):
+ """Compare paragraph counts between original and new document."""
+ original_count = self.count_paragraphs_in_original()
+ new_count = self.count_paragraphs_in_unpacked()
+
+ diff = new_count - original_count
+ diff_str = f"+{diff}" if diff > 0 else str(diff)
+ print(f"\nParagraphs: {original_count} → {new_count} ({diff_str})")
+
+
+if __name__ == "__main__":
+ raise RuntimeError("This module should not be run directly.")
diff --git a/scientific-skills/document-skills/pptx/ooxml/scripts/validation/pptx.py b/scientific-skills/document-skills/pptx/ooxml/scripts/validation/pptx.py
new file mode 100644
index 0000000..66d5b1e
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/scripts/validation/pptx.py
@@ -0,0 +1,315 @@
+"""
+Validator for PowerPoint presentation XML files against XSD schemas.
+"""
+
+import re
+
+from .base import BaseSchemaValidator
+
+
+class PPTXSchemaValidator(BaseSchemaValidator):
+ """Validator for PowerPoint presentation XML files against XSD schemas."""
+
+ # PowerPoint presentation namespace
+ PRESENTATIONML_NAMESPACE = (
+ "http://schemas.openxmlformats.org/presentationml/2006/main"
+ )
+
+ # PowerPoint-specific element to relationship type mappings
+ ELEMENT_RELATIONSHIP_TYPES = {
+ "sldid": "slide",
+ "sldmasterid": "slidemaster",
+ "notesmasterid": "notesmaster",
+ "sldlayoutid": "slidelayout",
+ "themeid": "theme",
+ "tablestyleid": "tablestyles",
+ }
+
+ def validate(self):
+ """Run all validation checks and return True if all pass."""
+ # Test 0: XML well-formedness
+ if not self.validate_xml():
+ return False
+
+ # Test 1: Namespace declarations
+ all_valid = True
+ if not self.validate_namespaces():
+ all_valid = False
+
+ # Test 2: Unique IDs
+ if not self.validate_unique_ids():
+ all_valid = False
+
+ # Test 3: UUID ID validation
+ if not self.validate_uuid_ids():
+ all_valid = False
+
+ # Test 4: Relationship and file reference validation
+ if not self.validate_file_references():
+ all_valid = False
+
+ # Test 5: Slide layout ID validation
+ if not self.validate_slide_layout_ids():
+ all_valid = False
+
+ # Test 6: Content type declarations
+ if not self.validate_content_types():
+ all_valid = False
+
+ # Test 7: XSD schema validation
+ if not self.validate_against_xsd():
+ all_valid = False
+
+ # Test 8: Notes slide reference validation
+ if not self.validate_notes_slide_references():
+ all_valid = False
+
+ # Test 9: Relationship ID reference validation
+ if not self.validate_all_relationship_ids():
+ all_valid = False
+
+ # Test 10: Duplicate slide layout references validation
+ if not self.validate_no_duplicate_slide_layouts():
+ all_valid = False
+
+ return all_valid
+
+ def validate_uuid_ids(self):
+ """Validate that ID attributes that look like UUIDs contain only hex values."""
+ import lxml.etree
+
+ errors = []
+ # UUID pattern: 8-4-4-4-12 hex digits with optional braces/hyphens
+ uuid_pattern = re.compile(
+ r"^[\{\(]?[0-9A-Fa-f]{8}-?[0-9A-Fa-f]{4}-?[0-9A-Fa-f]{4}-?[0-9A-Fa-f]{4}-?[0-9A-Fa-f]{12}[\}\)]?$"
+ )
+
+ for xml_file in self.xml_files:
+ try:
+ root = lxml.etree.parse(str(xml_file)).getroot()
+
+ # Check all elements for ID attributes
+ for elem in root.iter():
+ for attr, value in elem.attrib.items():
+ # Check if this is an ID attribute
+ attr_name = attr.split("}")[-1].lower()
+ if attr_name == "id" or attr_name.endswith("id"):
+ # Check if value looks like a UUID (has the right length and pattern structure)
+ if self._looks_like_uuid(value):
+ # Validate that it contains only hex characters in the right positions
+ if not uuid_pattern.match(value):
+ errors.append(
+ f" {xml_file.relative_to(self.unpacked_dir)}: "
+ f"Line {elem.sourceline}: ID '{value}' appears to be a UUID but contains invalid hex characters"
+ )
+
+ except (lxml.etree.XMLSyntaxError, Exception) as e:
+ errors.append(
+ f" {xml_file.relative_to(self.unpacked_dir)}: Error: {e}"
+ )
+
+ if errors:
+ print(f"FAILED - Found {len(errors)} UUID ID validation errors:")
+ for error in errors:
+ print(error)
+ return False
+ else:
+ if self.verbose:
+ print("PASSED - All UUID-like IDs contain valid hex values")
+ return True
+
+ def _looks_like_uuid(self, value):
+ """Check if a value has the general structure of a UUID."""
+ # Remove common UUID delimiters
+ clean_value = value.strip("{}()").replace("-", "")
+ # Check if it's 32 hex-like characters (could include invalid hex chars)
+ return len(clean_value) == 32 and all(c.isalnum() for c in clean_value)
+
+ def validate_slide_layout_ids(self):
+ """Validate that sldLayoutId elements in slide masters reference valid slide layouts."""
+ import lxml.etree
+
+ errors = []
+
+ # Find all slide master files
+ slide_masters = list(self.unpacked_dir.glob("ppt/slideMasters/*.xml"))
+
+ if not slide_masters:
+ if self.verbose:
+ print("PASSED - No slide masters found")
+ return True
+
+ for slide_master in slide_masters:
+ try:
+ # Parse the slide master file
+ root = lxml.etree.parse(str(slide_master)).getroot()
+
+ # Find the corresponding _rels file for this slide master
+ rels_file = slide_master.parent / "_rels" / f"{slide_master.name}.rels"
+
+ if not rels_file.exists():
+ errors.append(
+ f" {slide_master.relative_to(self.unpacked_dir)}: "
+ f"Missing relationships file: {rels_file.relative_to(self.unpacked_dir)}"
+ )
+ continue
+
+ # Parse the relationships file
+ rels_root = lxml.etree.parse(str(rels_file)).getroot()
+
+ # Build a set of valid relationship IDs that point to slide layouts
+ valid_layout_rids = set()
+ for rel in rels_root.findall(
+ f".//{{{self.PACKAGE_RELATIONSHIPS_NAMESPACE}}}Relationship"
+ ):
+ rel_type = rel.get("Type", "")
+ if "slideLayout" in rel_type:
+ valid_layout_rids.add(rel.get("Id"))
+
+ # Find all sldLayoutId elements in the slide master
+ for sld_layout_id in root.findall(
+ f".//{{{self.PRESENTATIONML_NAMESPACE}}}sldLayoutId"
+ ):
+ r_id = sld_layout_id.get(
+ f"{{{self.OFFICE_RELATIONSHIPS_NAMESPACE}}}id"
+ )
+ layout_id = sld_layout_id.get("id")
+
+ if r_id and r_id not in valid_layout_rids:
+ errors.append(
+ f" {slide_master.relative_to(self.unpacked_dir)}: "
+ f"Line {sld_layout_id.sourceline}: sldLayoutId with id='{layout_id}' "
+ f"references r:id='{r_id}' which is not found in slide layout relationships"
+ )
+
+ except (lxml.etree.XMLSyntaxError, Exception) as e:
+ errors.append(
+ f" {slide_master.relative_to(self.unpacked_dir)}: Error: {e}"
+ )
+
+ if errors:
+ print(f"FAILED - Found {len(errors)} slide layout ID validation errors:")
+ for error in errors:
+ print(error)
+ print(
+ "Remove invalid references or add missing slide layouts to the relationships file."
+ )
+ return False
+ else:
+ if self.verbose:
+ print("PASSED - All slide layout IDs reference valid slide layouts")
+ return True
+
+ def validate_no_duplicate_slide_layouts(self):
+ """Validate that each slide has exactly one slideLayout reference."""
+ import lxml.etree
+
+ errors = []
+ slide_rels_files = list(self.unpacked_dir.glob("ppt/slides/_rels/*.xml.rels"))
+
+ for rels_file in slide_rels_files:
+ try:
+ root = lxml.etree.parse(str(rels_file)).getroot()
+
+ # Find all slideLayout relationships
+ layout_rels = [
+ rel
+ for rel in root.findall(
+ f".//{{{self.PACKAGE_RELATIONSHIPS_NAMESPACE}}}Relationship"
+ )
+ if "slideLayout" in rel.get("Type", "")
+ ]
+
+ if len(layout_rels) > 1:
+ errors.append(
+ f" {rels_file.relative_to(self.unpacked_dir)}: has {len(layout_rels)} slideLayout references"
+ )
+
+ except Exception as e:
+ errors.append(
+ f" {rels_file.relative_to(self.unpacked_dir)}: Error: {e}"
+ )
+
+ if errors:
+ print("FAILED - Found slides with duplicate slideLayout references:")
+ for error in errors:
+ print(error)
+ return False
+ else:
+ if self.verbose:
+ print("PASSED - All slides have exactly one slideLayout reference")
+ return True
+
+ def validate_notes_slide_references(self):
+ """Validate that each notesSlide file is referenced by only one slide."""
+ import lxml.etree
+
+ errors = []
+ notes_slide_references = {} # Track which slides reference each notesSlide
+
+ # Find all slide relationship files
+ slide_rels_files = list(self.unpacked_dir.glob("ppt/slides/_rels/*.xml.rels"))
+
+ if not slide_rels_files:
+ if self.verbose:
+ print("PASSED - No slide relationship files found")
+ return True
+
+ for rels_file in slide_rels_files:
+ try:
+ # Parse the relationships file
+ root = lxml.etree.parse(str(rels_file)).getroot()
+
+ # Find all notesSlide relationships
+ for rel in root.findall(
+ f".//{{{self.PACKAGE_RELATIONSHIPS_NAMESPACE}}}Relationship"
+ ):
+ rel_type = rel.get("Type", "")
+ if "notesSlide" in rel_type:
+ target = rel.get("Target", "")
+ if target:
+ # Normalize the target path to handle relative paths
+ normalized_target = target.replace("../", "")
+
+ # Track which slide references this notesSlide
+ slide_name = rels_file.stem.replace(
+ ".xml", ""
+ ) # e.g., "slide1"
+
+ if normalized_target not in notes_slide_references:
+ notes_slide_references[normalized_target] = []
+ notes_slide_references[normalized_target].append(
+ (slide_name, rels_file)
+ )
+
+ except (lxml.etree.XMLSyntaxError, Exception) as e:
+ errors.append(
+ f" {rels_file.relative_to(self.unpacked_dir)}: Error: {e}"
+ )
+
+ # Check for duplicate references
+ for target, references in notes_slide_references.items():
+ if len(references) > 1:
+ slide_names = [ref[0] for ref in references]
+ errors.append(
+ f" Notes slide '{target}' is referenced by multiple slides: {', '.join(slide_names)}"
+ )
+ for slide_name, rels_file in references:
+ errors.append(f" - {rels_file.relative_to(self.unpacked_dir)}")
+
+ if errors:
+ print(
+ f"FAILED - Found {len([e for e in errors if not e.startswith(' ')])} notes slide reference validation errors:"
+ )
+ for error in errors:
+ print(error)
+ print("Each slide may optionally have its own slide file.")
+ return False
+ else:
+ if self.verbose:
+ print("PASSED - All notes slide references are unique")
+ return True
+
+
+if __name__ == "__main__":
+ raise RuntimeError("This module should not be run directly.")
diff --git a/scientific-skills/document-skills/pptx/ooxml/scripts/validation/redlining.py b/scientific-skills/document-skills/pptx/ooxml/scripts/validation/redlining.py
new file mode 100644
index 0000000..b389bc0
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/ooxml/scripts/validation/redlining.py
@@ -0,0 +1,279 @@
+"""
+Validator for tracked changes in Word documents.
+"""
+
+import subprocess
+import tempfile
+import zipfile
+from pathlib import Path
+
+
+class RedliningValidator:
+ """Validator for tracked changes in Word documents."""
+
+ def __init__(self, unpacked_dir, original_docx, verbose=False):
+ self.unpacked_dir = Path(unpacked_dir)
+ self.original_docx = Path(original_docx)
+ self.verbose = verbose
+ self.namespaces = {
+ "w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main"
+ }
+
+ def validate(self):
+ """Main validation method that returns True if valid, False otherwise."""
+ # Verify unpacked directory exists and has correct structure
+ modified_file = self.unpacked_dir / "word" / "document.xml"
+ if not modified_file.exists():
+ print(f"FAILED - Modified document.xml not found at {modified_file}")
+ return False
+
+ # First, check if there are any tracked changes by Scientific-Writer to validate
+ try:
+ import xml.etree.ElementTree as ET
+
+ tree = ET.parse(modified_file)
+ root = tree.getroot()
+
+ # Check for w:del or w:ins tags authored by Scientific-Writer
+ del_elements = root.findall(".//w:del", self.namespaces)
+ ins_elements = root.findall(".//w:ins", self.namespaces)
+
+ # Filter to only include changes by Scientific-Writer
+ sw_del_elements = [
+ elem
+ for elem in del_elements
+ if elem.get(f"{{{self.namespaces['w']}}}author") == "Scientific-Writer"
+ ]
+ sw_ins_elements = [
+ elem
+ for elem in ins_elements
+ if elem.get(f"{{{self.namespaces['w']}}}author") == "Scientific-Writer"
+ ]
+
+ # Redlining validation is only needed if tracked changes by Scientific-Writer have been used.
+ if not sw_del_elements and not sw_ins_elements:
+ if self.verbose:
+ print("PASSED - No tracked changes by Scientific-Writer found.")
+ return True
+
+ except Exception:
+ # If we can't parse the XML, continue with full validation
+ pass
+
+ # Create temporary directory for unpacking original docx
+ with tempfile.TemporaryDirectory() as temp_dir:
+ temp_path = Path(temp_dir)
+
+ # Unpack original docx
+ try:
+ with zipfile.ZipFile(self.original_docx, "r") as zip_ref:
+ zip_ref.extractall(temp_path)
+ except Exception as e:
+ print(f"FAILED - Error unpacking original docx: {e}")
+ return False
+
+ original_file = temp_path / "word" / "document.xml"
+ if not original_file.exists():
+ print(
+ f"FAILED - Original document.xml not found in {self.original_docx}"
+ )
+ return False
+
+ # Parse both XML files using xml.etree.ElementTree for redlining validation
+ try:
+ import xml.etree.ElementTree as ET
+
+ modified_tree = ET.parse(modified_file)
+ modified_root = modified_tree.getroot()
+ original_tree = ET.parse(original_file)
+ original_root = original_tree.getroot()
+ except ET.ParseError as e:
+ print(f"FAILED - Error parsing XML files: {e}")
+ return False
+
+ # Remove Scientific-Writer's tracked changes from both documents
+ self._remove_sw_tracked_changes(original_root)
+ self._remove_sw_tracked_changes(modified_root)
+
+ # Extract and compare text content
+ modified_text = self._extract_text_content(modified_root)
+ original_text = self._extract_text_content(original_root)
+
+ if modified_text != original_text:
+ # Show detailed character-level differences for each paragraph
+ error_message = self._generate_detailed_diff(
+ original_text, modified_text
+ )
+ print(error_message)
+ return False
+
+ if self.verbose:
+ print("PASSED - All changes by Scientific-Writer are properly tracked")
+ return True
+
+ def _generate_detailed_diff(self, original_text, modified_text):
+ """Generate detailed word-level differences using git word diff."""
+ error_parts = [
+ "FAILED - Document text doesn't match after removing Scientific-Writer's tracked changes",
+ "",
+ "Likely causes:",
+ " 1. Modified text inside another author's or tags",
+ " 2. Made edits without proper tracked changes",
+ " 3. Didn't nest inside when deleting another's insertion",
+ "",
+ "For pre-redlined documents, use correct patterns:",
+ " - To reject another's INSERTION: Nest inside their ",
+ " - To restore another's DELETION: Add new AFTER their ",
+ "",
+ ]
+
+ # Show git word diff
+ git_diff = self._get_git_word_diff(original_text, modified_text)
+ if git_diff:
+ error_parts.extend(["Differences:", "============", git_diff])
+ else:
+ error_parts.append("Unable to generate word diff (git not available)")
+
+ return "\n".join(error_parts)
+
+ def _get_git_word_diff(self, original_text, modified_text):
+ """Generate word diff using git with character-level precision."""
+ try:
+ with tempfile.TemporaryDirectory() as temp_dir:
+ temp_path = Path(temp_dir)
+
+ # Create two files
+ original_file = temp_path / "original.txt"
+ modified_file = temp_path / "modified.txt"
+
+ original_file.write_text(original_text, encoding="utf-8")
+ modified_file.write_text(modified_text, encoding="utf-8")
+
+ # Try character-level diff first for precise differences
+ result = subprocess.run(
+ [
+ "git",
+ "diff",
+ "--word-diff=plain",
+ "--word-diff-regex=.", # Character-by-character diff
+ "-U0", # Zero lines of context - show only changed lines
+ "--no-index",
+ str(original_file),
+ str(modified_file),
+ ],
+ capture_output=True,
+ text=True,
+ )
+
+ if result.stdout.strip():
+ # Clean up the output - remove git diff header lines
+ lines = result.stdout.split("\n")
+ # Skip the header lines (diff --git, index, +++, ---, @@)
+ content_lines = []
+ in_content = False
+ for line in lines:
+ if line.startswith("@@"):
+ in_content = True
+ continue
+ if in_content and line.strip():
+ content_lines.append(line)
+
+ if content_lines:
+ return "\n".join(content_lines)
+
+ # Fallback to word-level diff if character-level is too verbose
+ result = subprocess.run(
+ [
+ "git",
+ "diff",
+ "--word-diff=plain",
+ "-U0", # Zero lines of context
+ "--no-index",
+ str(original_file),
+ str(modified_file),
+ ],
+ capture_output=True,
+ text=True,
+ )
+
+ if result.stdout.strip():
+ lines = result.stdout.split("\n")
+ content_lines = []
+ in_content = False
+ for line in lines:
+ if line.startswith("@@"):
+ in_content = True
+ continue
+ if in_content and line.strip():
+ content_lines.append(line)
+ return "\n".join(content_lines)
+
+ except (subprocess.CalledProcessError, FileNotFoundError, Exception):
+ # Git not available or other error, return None to use fallback
+ pass
+
+ return None
+
+ def _remove_sw_tracked_changes(self, root):
+ """Remove tracked changes authored by Scientific-Writer from the XML root."""
+ ins_tag = f"{{{self.namespaces['w']}}}ins"
+ del_tag = f"{{{self.namespaces['w']}}}del"
+ author_attr = f"{{{self.namespaces['w']}}}author"
+
+ # Remove w:ins elements
+ for parent in root.iter():
+ to_remove = []
+ for child in parent:
+ if child.tag == ins_tag and child.get(author_attr) == "Scientific-Writer":
+ to_remove.append(child)
+ for elem in to_remove:
+ parent.remove(elem)
+
+ # Unwrap content in w:del elements where author is "Scientific-Writer"
+ deltext_tag = f"{{{self.namespaces['w']}}}delText"
+ t_tag = f"{{{self.namespaces['w']}}}t"
+
+ for parent in root.iter():
+ to_process = []
+ for child in parent:
+ if child.tag == del_tag and child.get(author_attr) == "Scientific-Writer":
+ to_process.append((child, list(parent).index(child)))
+
+ # Process in reverse order to maintain indices
+ for del_elem, del_index in reversed(to_process):
+ # Convert w:delText to w:t before moving
+ for elem in del_elem.iter():
+ if elem.tag == deltext_tag:
+ elem.tag = t_tag
+
+ # Move all children of w:del to its parent before removing w:del
+ for child in reversed(list(del_elem)):
+ parent.insert(del_index, child)
+ parent.remove(del_elem)
+
+ def _extract_text_content(self, root):
+ """Extract text content from Word XML, preserving paragraph structure.
+
+ Empty paragraphs are skipped to avoid false positives when tracked
+ insertions add only structural elements without text content.
+ """
+ p_tag = f"{{{self.namespaces['w']}}}p"
+ t_tag = f"{{{self.namespaces['w']}}}t"
+
+ paragraphs = []
+ for p_elem in root.findall(f".//{p_tag}"):
+ # Get all text elements within this paragraph
+ text_parts = []
+ for t_elem in p_elem.findall(f".//{t_tag}"):
+ if t_elem.text:
+ text_parts.append(t_elem.text)
+ paragraph_text = "".join(text_parts)
+ # Skip empty paragraphs - they don't affect content validation
+ if paragraph_text:
+ paragraphs.append(paragraph_text)
+
+ return "\n".join(paragraphs)
+
+
+if __name__ == "__main__":
+ raise RuntimeError("This module should not be run directly.")
diff --git a/scientific-skills/document-skills/pptx/scripts/html2pptx.js b/scientific-skills/document-skills/pptx/scripts/html2pptx.js
new file mode 100755
index 0000000..437bf7c
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/scripts/html2pptx.js
@@ -0,0 +1,979 @@
+/**
+ * html2pptx - Convert HTML slide to pptxgenjs slide with positioned elements
+ *
+ * USAGE:
+ * const pptx = new pptxgen();
+ * pptx.layout = 'LAYOUT_16x9'; // Must match HTML body dimensions
+ *
+ * const { slide, placeholders } = await html2pptx('slide.html', pptx);
+ * slide.addChart(pptx.charts.LINE, data, placeholders[0]);
+ *
+ * await pptx.writeFile('output.pptx');
+ *
+ * FEATURES:
+ * - Converts HTML to PowerPoint with accurate positioning
+ * - Supports text, images, shapes, and bullet lists
+ * - Extracts placeholder elements (class="placeholder") with positions
+ * - Handles CSS gradients, borders, and margins
+ *
+ * VALIDATION:
+ * - Uses body width/height from HTML for viewport sizing
+ * - Throws error if HTML dimensions don't match presentation layout
+ * - Throws error if content overflows body (with overflow details)
+ *
+ * RETURNS:
+ * { slide, placeholders } where placeholders is an array of { id, x, y, w, h }
+ */
+
+const { chromium } = require('playwright');
+const path = require('path');
+const sharp = require('sharp');
+
+const PT_PER_PX = 0.75;
+const PX_PER_IN = 96;
+const EMU_PER_IN = 914400;
+
+// Helper: Get body dimensions and check for overflow
+async function getBodyDimensions(page) {
+ const bodyDimensions = await page.evaluate(() => {
+ const body = document.body;
+ const style = window.getComputedStyle(body);
+
+ return {
+ width: parseFloat(style.width),
+ height: parseFloat(style.height),
+ scrollWidth: body.scrollWidth,
+ scrollHeight: body.scrollHeight
+ };
+ });
+
+ const errors = [];
+ const widthOverflowPx = Math.max(0, bodyDimensions.scrollWidth - bodyDimensions.width - 1);
+ const heightOverflowPx = Math.max(0, bodyDimensions.scrollHeight - bodyDimensions.height - 1);
+
+ const widthOverflowPt = widthOverflowPx * PT_PER_PX;
+ const heightOverflowPt = heightOverflowPx * PT_PER_PX;
+
+ if (widthOverflowPt > 0 || heightOverflowPt > 0) {
+ const directions = [];
+ if (widthOverflowPt > 0) directions.push(`${widthOverflowPt.toFixed(1)}pt horizontally`);
+ if (heightOverflowPt > 0) directions.push(`${heightOverflowPt.toFixed(1)}pt vertically`);
+ const reminder = heightOverflowPt > 0 ? ' (Remember: leave 0.5" margin at bottom of slide)' : '';
+ errors.push(`HTML content overflows body by ${directions.join(' and ')}${reminder}`);
+ }
+
+ return { ...bodyDimensions, errors };
+}
+
+// Helper: Validate dimensions match presentation layout
+function validateDimensions(bodyDimensions, pres) {
+ const errors = [];
+ const widthInches = bodyDimensions.width / PX_PER_IN;
+ const heightInches = bodyDimensions.height / PX_PER_IN;
+
+ if (pres.presLayout) {
+ const layoutWidth = pres.presLayout.width / EMU_PER_IN;
+ const layoutHeight = pres.presLayout.height / EMU_PER_IN;
+
+ if (Math.abs(layoutWidth - widthInches) > 0.1 || Math.abs(layoutHeight - heightInches) > 0.1) {
+ errors.push(
+ `HTML dimensions (${widthInches.toFixed(1)}" × ${heightInches.toFixed(1)}") ` +
+ `don't match presentation layout (${layoutWidth.toFixed(1)}" × ${layoutHeight.toFixed(1)}")`
+ );
+ }
+ }
+ return errors;
+}
+
+function validateTextBoxPosition(slideData, bodyDimensions) {
+ const errors = [];
+ const slideHeightInches = bodyDimensions.height / PX_PER_IN;
+ const minBottomMargin = 0.5; // 0.5 inches from bottom
+
+ for (const el of slideData.elements) {
+ // Check text elements (p, h1-h6, list)
+ if (['p', 'h1', 'h2', 'h3', 'h4', 'h5', 'h6', 'list'].includes(el.type)) {
+ const fontSize = el.style?.fontSize || 0;
+ const bottomEdge = el.position.y + el.position.h;
+ const distanceFromBottom = slideHeightInches - bottomEdge;
+
+ if (fontSize > 12 && distanceFromBottom < minBottomMargin) {
+ const getText = () => {
+ if (typeof el.text === 'string') return el.text;
+ if (Array.isArray(el.text)) return el.text.find(t => t.text)?.text || '';
+ if (Array.isArray(el.items)) return el.items.find(item => item.text)?.text || '';
+ return '';
+ };
+ const textPrefix = getText().substring(0, 50) + (getText().length > 50 ? '...' : '');
+
+ errors.push(
+ `Text box "${textPrefix}" ends too close to bottom edge ` +
+ `(${distanceFromBottom.toFixed(2)}" from bottom, minimum ${minBottomMargin}" required)`
+ );
+ }
+ }
+ }
+
+ return errors;
+}
+
+// Helper: Add background to slide
+async function addBackground(slideData, targetSlide, tmpDir) {
+ if (slideData.background.type === 'image' && slideData.background.path) {
+ let imagePath = slideData.background.path.startsWith('file://')
+ ? slideData.background.path.replace('file://', '')
+ : slideData.background.path;
+ targetSlide.background = { path: imagePath };
+ } else if (slideData.background.type === 'color' && slideData.background.value) {
+ targetSlide.background = { color: slideData.background.value };
+ }
+}
+
+// Helper: Add elements to slide
+function addElements(slideData, targetSlide, pres) {
+ for (const el of slideData.elements) {
+ if (el.type === 'image') {
+ let imagePath = el.src.startsWith('file://') ? el.src.replace('file://', '') : el.src;
+ targetSlide.addImage({
+ path: imagePath,
+ x: el.position.x,
+ y: el.position.y,
+ w: el.position.w,
+ h: el.position.h
+ });
+ } else if (el.type === 'line') {
+ targetSlide.addShape(pres.ShapeType.line, {
+ x: el.x1,
+ y: el.y1,
+ w: el.x2 - el.x1,
+ h: el.y2 - el.y1,
+ line: { color: el.color, width: el.width }
+ });
+ } else if (el.type === 'shape') {
+ const shapeOptions = {
+ x: el.position.x,
+ y: el.position.y,
+ w: el.position.w,
+ h: el.position.h,
+ shape: el.shape.rectRadius > 0 ? pres.ShapeType.roundRect : pres.ShapeType.rect
+ };
+
+ if (el.shape.fill) {
+ shapeOptions.fill = { color: el.shape.fill };
+ if (el.shape.transparency != null) shapeOptions.fill.transparency = el.shape.transparency;
+ }
+ if (el.shape.line) shapeOptions.line = el.shape.line;
+ if (el.shape.rectRadius > 0) shapeOptions.rectRadius = el.shape.rectRadius;
+ if (el.shape.shadow) shapeOptions.shadow = el.shape.shadow;
+
+ targetSlide.addText(el.text || '', shapeOptions);
+ } else if (el.type === 'list') {
+ const listOptions = {
+ x: el.position.x,
+ y: el.position.y,
+ w: el.position.w,
+ h: el.position.h,
+ fontSize: el.style.fontSize,
+ fontFace: el.style.fontFace,
+ color: el.style.color,
+ align: el.style.align,
+ valign: 'top',
+ lineSpacing: el.style.lineSpacing,
+ paraSpaceBefore: el.style.paraSpaceBefore,
+ paraSpaceAfter: el.style.paraSpaceAfter,
+ margin: el.style.margin
+ };
+ if (el.style.margin) listOptions.margin = el.style.margin;
+ targetSlide.addText(el.items, listOptions);
+ } else {
+ // Check if text is single-line (height suggests one line)
+ const lineHeight = el.style.lineSpacing || el.style.fontSize * 1.2;
+ const isSingleLine = el.position.h <= lineHeight * 1.5;
+
+ let adjustedX = el.position.x;
+ let adjustedW = el.position.w;
+
+ // Make single-line text 2% wider to account for underestimate
+ if (isSingleLine) {
+ const widthIncrease = el.position.w * 0.02;
+ const align = el.style.align;
+
+ if (align === 'center') {
+ // Center: expand both sides
+ adjustedX = el.position.x - (widthIncrease / 2);
+ adjustedW = el.position.w + widthIncrease;
+ } else if (align === 'right') {
+ // Right: expand to the left
+ adjustedX = el.position.x - widthIncrease;
+ adjustedW = el.position.w + widthIncrease;
+ } else {
+ // Left (default): expand to the right
+ adjustedW = el.position.w + widthIncrease;
+ }
+ }
+
+ const textOptions = {
+ x: adjustedX,
+ y: el.position.y,
+ w: adjustedW,
+ h: el.position.h,
+ fontSize: el.style.fontSize,
+ fontFace: el.style.fontFace,
+ color: el.style.color,
+ bold: el.style.bold,
+ italic: el.style.italic,
+ underline: el.style.underline,
+ valign: 'top',
+ lineSpacing: el.style.lineSpacing,
+ paraSpaceBefore: el.style.paraSpaceBefore,
+ paraSpaceAfter: el.style.paraSpaceAfter,
+ inset: 0 // Remove default PowerPoint internal padding
+ };
+
+ if (el.style.align) textOptions.align = el.style.align;
+ if (el.style.margin) textOptions.margin = el.style.margin;
+ if (el.style.rotate !== undefined) textOptions.rotate = el.style.rotate;
+ if (el.style.transparency !== null && el.style.transparency !== undefined) textOptions.transparency = el.style.transparency;
+
+ targetSlide.addText(el.text, textOptions);
+ }
+ }
+}
+
+// Helper: Extract slide data from HTML page
+async function extractSlideData(page) {
+ return await page.evaluate(() => {
+ const PT_PER_PX = 0.75;
+ const PX_PER_IN = 96;
+
+ // Fonts that are single-weight and should not have bold applied
+ // (applying bold causes PowerPoint to use faux bold which makes text wider)
+ const SINGLE_WEIGHT_FONTS = ['impact'];
+
+ // Helper: Check if a font should skip bold formatting
+ const shouldSkipBold = (fontFamily) => {
+ if (!fontFamily) return false;
+ const normalizedFont = fontFamily.toLowerCase().replace(/['"]/g, '').split(',')[0].trim();
+ return SINGLE_WEIGHT_FONTS.includes(normalizedFont);
+ };
+
+ // Unit conversion helpers
+ const pxToInch = (px) => px / PX_PER_IN;
+ const pxToPoints = (pxStr) => parseFloat(pxStr) * PT_PER_PX;
+ const rgbToHex = (rgbStr) => {
+ // Handle transparent backgrounds by defaulting to white
+ if (rgbStr === 'rgba(0, 0, 0, 0)' || rgbStr === 'transparent') return 'FFFFFF';
+
+ const match = rgbStr.match(/rgba?\((\d+),\s*(\d+),\s*(\d+)/);
+ if (!match) return 'FFFFFF';
+ return match.slice(1).map(n => parseInt(n).toString(16).padStart(2, '0')).join('');
+ };
+
+ const extractAlpha = (rgbStr) => {
+ const match = rgbStr.match(/rgba\((\d+),\s*(\d+),\s*(\d+),\s*([\d.]+)\)/);
+ if (!match || !match[4]) return null;
+ const alpha = parseFloat(match[4]);
+ return Math.round((1 - alpha) * 100);
+ };
+
+ const applyTextTransform = (text, textTransform) => {
+ if (textTransform === 'uppercase') return text.toUpperCase();
+ if (textTransform === 'lowercase') return text.toLowerCase();
+ if (textTransform === 'capitalize') {
+ return text.replace(/\b\w/g, c => c.toUpperCase());
+ }
+ return text;
+ };
+
+ // Extract rotation angle from CSS transform and writing-mode
+ const getRotation = (transform, writingMode) => {
+ let angle = 0;
+
+ // Handle writing-mode first
+ // PowerPoint: 90° = text rotated 90° clockwise (reads top to bottom, letters upright)
+ // PowerPoint: 270° = text rotated 270° clockwise (reads bottom to top, letters upright)
+ if (writingMode === 'vertical-rl') {
+ // vertical-rl alone = text reads top to bottom = 90° in PowerPoint
+ angle = 90;
+ } else if (writingMode === 'vertical-lr') {
+ // vertical-lr alone = text reads bottom to top = 270° in PowerPoint
+ angle = 270;
+ }
+
+ // Then add any transform rotation
+ if (transform && transform !== 'none') {
+ // Try to match rotate() function
+ const rotateMatch = transform.match(/rotate\((-?\d+(?:\.\d+)?)deg\)/);
+ if (rotateMatch) {
+ angle += parseFloat(rotateMatch[1]);
+ } else {
+ // Browser may compute as matrix - extract rotation from matrix
+ const matrixMatch = transform.match(/matrix\(([^)]+)\)/);
+ if (matrixMatch) {
+ const values = matrixMatch[1].split(',').map(parseFloat);
+ // matrix(a, b, c, d, e, f) where rotation = atan2(b, a)
+ const matrixAngle = Math.atan2(values[1], values[0]) * (180 / Math.PI);
+ angle += Math.round(matrixAngle);
+ }
+ }
+ }
+
+ // Normalize to 0-359 range
+ angle = angle % 360;
+ if (angle < 0) angle += 360;
+
+ return angle === 0 ? null : angle;
+ };
+
+ // Get position/dimensions accounting for rotation
+ const getPositionAndSize = (el, rect, rotation) => {
+ if (rotation === null) {
+ return { x: rect.left, y: rect.top, w: rect.width, h: rect.height };
+ }
+
+ // For 90° or 270° rotations, swap width and height
+ // because PowerPoint applies rotation to the original (unrotated) box
+ const isVertical = rotation === 90 || rotation === 270;
+
+ if (isVertical) {
+ // The browser shows us the rotated dimensions (tall box for vertical text)
+ // But PowerPoint needs the pre-rotation dimensions (wide box that will be rotated)
+ // So we swap: browser's height becomes PPT's width, browser's width becomes PPT's height
+ const centerX = rect.left + rect.width / 2;
+ const centerY = rect.top + rect.height / 2;
+
+ return {
+ x: centerX - rect.height / 2,
+ y: centerY - rect.width / 2,
+ w: rect.height,
+ h: rect.width
+ };
+ }
+
+ // For other rotations, use element's offset dimensions
+ const centerX = rect.left + rect.width / 2;
+ const centerY = rect.top + rect.height / 2;
+ return {
+ x: centerX - el.offsetWidth / 2,
+ y: centerY - el.offsetHeight / 2,
+ w: el.offsetWidth,
+ h: el.offsetHeight
+ };
+ };
+
+ // Parse CSS box-shadow into PptxGenJS shadow properties
+ const parseBoxShadow = (boxShadow) => {
+ if (!boxShadow || boxShadow === 'none') return null;
+
+ // Browser computed style format: "rgba(0, 0, 0, 0.3) 2px 2px 8px 0px [inset]"
+ // CSS format: "[inset] 2px 2px 8px 0px rgba(0, 0, 0, 0.3)"
+
+ const insetMatch = boxShadow.match(/inset/);
+
+ // IMPORTANT: PptxGenJS/PowerPoint doesn't properly support inset shadows
+ // Only process outer shadows to avoid file corruption
+ if (insetMatch) return null;
+
+ // Extract color first (rgba or rgb at start)
+ const colorMatch = boxShadow.match(/rgba?\([^)]+\)/);
+
+ // Extract numeric values (handles both px and pt units)
+ const parts = boxShadow.match(/([-\d.]+)(px|pt)/g);
+
+ if (!parts || parts.length < 2) return null;
+
+ const offsetX = parseFloat(parts[0]);
+ const offsetY = parseFloat(parts[1]);
+ const blur = parts.length > 2 ? parseFloat(parts[2]) : 0;
+
+ // Calculate angle from offsets (in degrees, 0 = right, 90 = down)
+ let angle = 0;
+ if (offsetX !== 0 || offsetY !== 0) {
+ angle = Math.atan2(offsetY, offsetX) * (180 / Math.PI);
+ if (angle < 0) angle += 360;
+ }
+
+ // Calculate offset distance (hypotenuse)
+ const offset = Math.sqrt(offsetX * offsetX + offsetY * offsetY) * PT_PER_PX;
+
+ // Extract opacity from rgba
+ let opacity = 0.5;
+ if (colorMatch) {
+ const opacityMatch = colorMatch[0].match(/[\d.]+\)$/);
+ if (opacityMatch) {
+ opacity = parseFloat(opacityMatch[0].replace(')', ''));
+ }
+ }
+
+ return {
+ type: 'outer',
+ angle: Math.round(angle),
+ blur: blur * 0.75, // Convert to points
+ color: colorMatch ? rgbToHex(colorMatch[0]) : '000000',
+ offset: offset,
+ opacity
+ };
+ };
+
+ // Parse inline formatting tags (, , , , , ) into text runs
+ const parseInlineFormatting = (element, baseOptions = {}, runs = [], baseTextTransform = (x) => x) => {
+ let prevNodeIsText = false;
+
+ element.childNodes.forEach((node) => {
+ let textTransform = baseTextTransform;
+
+ const isText = node.nodeType === Node.TEXT_NODE || node.tagName === 'BR';
+ if (isText) {
+ const text = node.tagName === 'BR' ? '\n' : textTransform(node.textContent.replace(/\s+/g, ' '));
+ const prevRun = runs[runs.length - 1];
+ if (prevNodeIsText && prevRun) {
+ prevRun.text += text;
+ } else {
+ runs.push({ text, options: { ...baseOptions } });
+ }
+
+ } else if (node.nodeType === Node.ELEMENT_NODE && node.textContent.trim()) {
+ const options = { ...baseOptions };
+ const computed = window.getComputedStyle(node);
+
+ // Handle inline elements with computed styles
+ if (node.tagName === 'SPAN' || node.tagName === 'B' || node.tagName === 'STRONG' || node.tagName === 'I' || node.tagName === 'EM' || node.tagName === 'U') {
+ const isBold = computed.fontWeight === 'bold' || parseInt(computed.fontWeight) >= 600;
+ if (isBold && !shouldSkipBold(computed.fontFamily)) options.bold = true;
+ if (computed.fontStyle === 'italic') options.italic = true;
+ if (computed.textDecoration && computed.textDecoration.includes('underline')) options.underline = true;
+ if (computed.color && computed.color !== 'rgb(0, 0, 0)') {
+ options.color = rgbToHex(computed.color);
+ const transparency = extractAlpha(computed.color);
+ if (transparency !== null) options.transparency = transparency;
+ }
+ if (computed.fontSize) options.fontSize = pxToPoints(computed.fontSize);
+
+ // Apply text-transform on the span element itself
+ if (computed.textTransform && computed.textTransform !== 'none') {
+ const transformStr = computed.textTransform;
+ textTransform = (text) => applyTextTransform(text, transformStr);
+ }
+
+ // Validate: Check for margins on inline elements
+ if (computed.marginLeft && parseFloat(computed.marginLeft) > 0) {
+ errors.push(`Inline element <${node.tagName.toLowerCase()}> has margin-left which is not supported in PowerPoint. Remove margin from inline elements.`);
+ }
+ if (computed.marginRight && parseFloat(computed.marginRight) > 0) {
+ errors.push(`Inline element <${node.tagName.toLowerCase()}> has margin-right which is not supported in PowerPoint. Remove margin from inline elements.`);
+ }
+ if (computed.marginTop && parseFloat(computed.marginTop) > 0) {
+ errors.push(`Inline element <${node.tagName.toLowerCase()}> has margin-top which is not supported in PowerPoint. Remove margin from inline elements.`);
+ }
+ if (computed.marginBottom && parseFloat(computed.marginBottom) > 0) {
+ errors.push(`Inline element <${node.tagName.toLowerCase()}> has margin-bottom which is not supported in PowerPoint. Remove margin from inline elements.`);
+ }
+
+ // Recursively process the child node. This will flatten nested spans into multiple runs.
+ parseInlineFormatting(node, options, runs, textTransform);
+ }
+ }
+
+ prevNodeIsText = isText;
+ });
+
+ // Trim leading space from first run and trailing space from last run
+ if (runs.length > 0) {
+ runs[0].text = runs[0].text.replace(/^\s+/, '');
+ runs[runs.length - 1].text = runs[runs.length - 1].text.replace(/\s+$/, '');
+ }
+
+ return runs.filter(r => r.text.length > 0);
+ };
+
+ // Extract background from body (image or color)
+ const body = document.body;
+ const bodyStyle = window.getComputedStyle(body);
+ const bgImage = bodyStyle.backgroundImage;
+ const bgColor = bodyStyle.backgroundColor;
+
+ // Collect validation errors
+ const errors = [];
+
+ // Validate: Check for CSS gradients
+ if (bgImage && (bgImage.includes('linear-gradient') || bgImage.includes('radial-gradient'))) {
+ errors.push(
+ 'CSS gradients are not supported. Use Sharp to rasterize gradients as PNG images first, ' +
+ 'then reference with background-image: url(\'gradient.png\')'
+ );
+ }
+
+ let background;
+ if (bgImage && bgImage !== 'none') {
+ // Extract URL from url("...") or url(...)
+ const urlMatch = bgImage.match(/url\(["']?([^"')]+)["']?\)/);
+ if (urlMatch) {
+ background = {
+ type: 'image',
+ path: urlMatch[1]
+ };
+ } else {
+ background = {
+ type: 'color',
+ value: rgbToHex(bgColor)
+ };
+ }
+ } else {
+ background = {
+ type: 'color',
+ value: rgbToHex(bgColor)
+ };
+ }
+
+ // Process all elements
+ const elements = [];
+ const placeholders = [];
+ const textTags = ['P', 'H1', 'H2', 'H3', 'H4', 'H5', 'H6', 'UL', 'OL', 'LI'];
+ const processed = new Set();
+
+ document.querySelectorAll('*').forEach((el) => {
+ if (processed.has(el)) return;
+
+ // Validate text elements don't have backgrounds, borders, or shadows
+ if (textTags.includes(el.tagName)) {
+ const computed = window.getComputedStyle(el);
+ const hasBg = computed.backgroundColor && computed.backgroundColor !== 'rgba(0, 0, 0, 0)';
+ const hasBorder = (computed.borderWidth && parseFloat(computed.borderWidth) > 0) ||
+ (computed.borderTopWidth && parseFloat(computed.borderTopWidth) > 0) ||
+ (computed.borderRightWidth && parseFloat(computed.borderRightWidth) > 0) ||
+ (computed.borderBottomWidth && parseFloat(computed.borderBottomWidth) > 0) ||
+ (computed.borderLeftWidth && parseFloat(computed.borderLeftWidth) > 0);
+ const hasShadow = computed.boxShadow && computed.boxShadow !== 'none';
+
+ if (hasBg || hasBorder || hasShadow) {
+ errors.push(
+ `Text element <${el.tagName.toLowerCase()}> has ${hasBg ? 'background' : hasBorder ? 'border' : 'shadow'}. ` +
+ 'Backgrounds, borders, and shadows are only supported on elements, not text elements.'
+ );
+ return;
+ }
+ }
+
+ // Extract placeholder elements (for charts, etc.)
+ if (el.className && el.className.includes('placeholder')) {
+ const rect = el.getBoundingClientRect();
+ if (rect.width === 0 || rect.height === 0) {
+ errors.push(
+ `Placeholder "${el.id || 'unnamed'}" has ${rect.width === 0 ? 'width: 0' : 'height: 0'}. Check the layout CSS.`
+ );
+ } else {
+ placeholders.push({
+ id: el.id || `placeholder-${placeholders.length}`,
+ x: pxToInch(rect.left),
+ y: pxToInch(rect.top),
+ w: pxToInch(rect.width),
+ h: pxToInch(rect.height)
+ });
+ }
+ processed.add(el);
+ return;
+ }
+
+ // Extract images
+ if (el.tagName === 'IMG') {
+ const rect = el.getBoundingClientRect();
+ if (rect.width > 0 && rect.height > 0) {
+ elements.push({
+ type: 'image',
+ src: el.src,
+ position: {
+ x: pxToInch(rect.left),
+ y: pxToInch(rect.top),
+ w: pxToInch(rect.width),
+ h: pxToInch(rect.height)
+ }
+ });
+ processed.add(el);
+ return;
+ }
+ }
+
+ // Extract DIVs with backgrounds/borders as shapes
+ const isContainer = el.tagName === 'DIV' && !textTags.includes(el.tagName);
+ if (isContainer) {
+ const computed = window.getComputedStyle(el);
+ const hasBg = computed.backgroundColor && computed.backgroundColor !== 'rgba(0, 0, 0, 0)';
+
+ // Validate: Check for unwrapped text content in DIV
+ for (const node of el.childNodes) {
+ if (node.nodeType === Node.TEXT_NODE) {
+ const text = node.textContent.trim();
+ if (text) {
+ errors.push(
+ `DIV element contains unwrapped text "${text.substring(0, 50)}${text.length > 50 ? '...' : ''}". ` +
+ 'All text must be wrapped in
,
-, , or tags to appear in PowerPoint.'
+ );
+ }
+ }
+ }
+
+ // Check for background images on shapes
+ const bgImage = computed.backgroundImage;
+ if (bgImage && bgImage !== 'none') {
+ errors.push(
+ 'Background images on DIV elements are not supported. ' +
+ 'Use solid colors or borders for shapes, or use slide.addImage() in PptxGenJS to layer images.'
+ );
+ return;
+ }
+
+ // Check for borders - both uniform and partial
+ const borderTop = computed.borderTopWidth;
+ const borderRight = computed.borderRightWidth;
+ const borderBottom = computed.borderBottomWidth;
+ const borderLeft = computed.borderLeftWidth;
+ const borders = [borderTop, borderRight, borderBottom, borderLeft].map(b => parseFloat(b) || 0);
+ const hasBorder = borders.some(b => b > 0);
+ const hasUniformBorder = hasBorder && borders.every(b => b === borders[0]);
+ const borderLines = [];
+
+ if (hasBorder && !hasUniformBorder) {
+ const rect = el.getBoundingClientRect();
+ const x = pxToInch(rect.left);
+ const y = pxToInch(rect.top);
+ const w = pxToInch(rect.width);
+ const h = pxToInch(rect.height);
+
+ // Collect lines to add after shape (inset by half the line width to center on edge)
+ if (parseFloat(borderTop) > 0) {
+ const widthPt = pxToPoints(borderTop);
+ const inset = (widthPt / 72) / 2; // Convert points to inches, then half
+ borderLines.push({
+ type: 'line',
+ x1: x, y1: y + inset, x2: x + w, y2: y + inset,
+ width: widthPt,
+ color: rgbToHex(computed.borderTopColor)
+ });
+ }
+ if (parseFloat(borderRight) > 0) {
+ const widthPt = pxToPoints(borderRight);
+ const inset = (widthPt / 72) / 2;
+ borderLines.push({
+ type: 'line',
+ x1: x + w - inset, y1: y, x2: x + w - inset, y2: y + h,
+ width: widthPt,
+ color: rgbToHex(computed.borderRightColor)
+ });
+ }
+ if (parseFloat(borderBottom) > 0) {
+ const widthPt = pxToPoints(borderBottom);
+ const inset = (widthPt / 72) / 2;
+ borderLines.push({
+ type: 'line',
+ x1: x, y1: y + h - inset, x2: x + w, y2: y + h - inset,
+ width: widthPt,
+ color: rgbToHex(computed.borderBottomColor)
+ });
+ }
+ if (parseFloat(borderLeft) > 0) {
+ const widthPt = pxToPoints(borderLeft);
+ const inset = (widthPt / 72) / 2;
+ borderLines.push({
+ type: 'line',
+ x1: x + inset, y1: y, x2: x + inset, y2: y + h,
+ width: widthPt,
+ color: rgbToHex(computed.borderLeftColor)
+ });
+ }
+ }
+
+ if (hasBg || hasBorder) {
+ const rect = el.getBoundingClientRect();
+ if (rect.width > 0 && rect.height > 0) {
+ const shadow = parseBoxShadow(computed.boxShadow);
+
+ // Only add shape if there's background or uniform border
+ if (hasBg || hasUniformBorder) {
+ elements.push({
+ type: 'shape',
+ text: '', // Shape only - child text elements render on top
+ position: {
+ x: pxToInch(rect.left),
+ y: pxToInch(rect.top),
+ w: pxToInch(rect.width),
+ h: pxToInch(rect.height)
+ },
+ shape: {
+ fill: hasBg ? rgbToHex(computed.backgroundColor) : null,
+ transparency: hasBg ? extractAlpha(computed.backgroundColor) : null,
+ line: hasUniformBorder ? {
+ color: rgbToHex(computed.borderColor),
+ width: pxToPoints(computed.borderWidth)
+ } : null,
+ // Convert border-radius to rectRadius (in inches)
+ // % values: 50%+ = circle (1), <50% = percentage of min dimension
+ // pt values: divide by 72 (72pt = 1 inch)
+ // px values: divide by 96 (96px = 1 inch)
+ rectRadius: (() => {
+ const radius = computed.borderRadius;
+ const radiusValue = parseFloat(radius);
+ if (radiusValue === 0) return 0;
+
+ if (radius.includes('%')) {
+ if (radiusValue >= 50) return 1;
+ // Calculate percentage of smaller dimension
+ const minDim = Math.min(rect.width, rect.height);
+ return (radiusValue / 100) * pxToInch(minDim);
+ }
+
+ if (radius.includes('pt')) return radiusValue / 72;
+ return radiusValue / PX_PER_IN;
+ })(),
+ shadow: shadow
+ }
+ });
+ }
+
+ // Add partial border lines
+ elements.push(...borderLines);
+
+ processed.add(el);
+ return;
+ }
+ }
+ }
+
+ // Extract bullet lists as single text block
+ if (el.tagName === 'UL' || el.tagName === 'OL') {
+ const rect = el.getBoundingClientRect();
+ if (rect.width === 0 || rect.height === 0) return;
+
+ const liElements = Array.from(el.querySelectorAll('li'));
+ const items = [];
+ const ulComputed = window.getComputedStyle(el);
+ const ulPaddingLeftPt = pxToPoints(ulComputed.paddingLeft);
+
+ // Split: margin-left for bullet position, indent for text position
+ // margin-left + indent = ul padding-left
+ const marginLeft = ulPaddingLeftPt * 0.5;
+ const textIndent = ulPaddingLeftPt * 0.5;
+
+ liElements.forEach((li, idx) => {
+ const isLast = idx === liElements.length - 1;
+ const runs = parseInlineFormatting(li, { breakLine: false });
+ // Clean manual bullets from first run
+ if (runs.length > 0) {
+ runs[0].text = runs[0].text.replace(/^[•\-\*▪▸]\s*/, '');
+ runs[0].options.bullet = { indent: textIndent };
+ }
+ // Set breakLine on last run
+ if (runs.length > 0 && !isLast) {
+ runs[runs.length - 1].options.breakLine = true;
+ }
+ items.push(...runs);
+ });
+
+ const computed = window.getComputedStyle(liElements[0] || el);
+
+ elements.push({
+ type: 'list',
+ items: items,
+ position: {
+ x: pxToInch(rect.left),
+ y: pxToInch(rect.top),
+ w: pxToInch(rect.width),
+ h: pxToInch(rect.height)
+ },
+ style: {
+ fontSize: pxToPoints(computed.fontSize),
+ fontFace: computed.fontFamily.split(',')[0].replace(/['"]/g, '').trim(),
+ color: rgbToHex(computed.color),
+ transparency: extractAlpha(computed.color),
+ align: computed.textAlign === 'start' ? 'left' : computed.textAlign,
+ lineSpacing: computed.lineHeight && computed.lineHeight !== 'normal' ? pxToPoints(computed.lineHeight) : null,
+ paraSpaceBefore: 0,
+ paraSpaceAfter: pxToPoints(computed.marginBottom),
+ // PptxGenJS margin array is [left, right, bottom, top]
+ margin: [marginLeft, 0, 0, 0]
+ }
+ });
+
+ liElements.forEach(li => processed.add(li));
+ processed.add(el);
+ return;
+ }
+
+ // Extract text elements (P, H1, H2, etc.)
+ if (!textTags.includes(el.tagName)) return;
+
+ const rect = el.getBoundingClientRect();
+ const text = el.textContent.trim();
+ if (rect.width === 0 || rect.height === 0 || !text) return;
+
+ // Validate: Check for manual bullet symbols in text elements (not in lists)
+ if (el.tagName !== 'LI' && /^[•\-\*▪▸○●◆◇■□]\s/.test(text.trimStart())) {
+ errors.push(
+ `Text element <${el.tagName.toLowerCase()}> starts with bullet symbol "${text.substring(0, 20)}...". ` +
+ 'Use or lists instead of manual bullet symbols.'
+ );
+ return;
+ }
+
+ const computed = window.getComputedStyle(el);
+ const rotation = getRotation(computed.transform, computed.writingMode);
+ const { x, y, w, h } = getPositionAndSize(el, rect, rotation);
+
+ const baseStyle = {
+ fontSize: pxToPoints(computed.fontSize),
+ fontFace: computed.fontFamily.split(',')[0].replace(/['"]/g, '').trim(),
+ color: rgbToHex(computed.color),
+ align: computed.textAlign === 'start' ? 'left' : computed.textAlign,
+ lineSpacing: pxToPoints(computed.lineHeight),
+ paraSpaceBefore: pxToPoints(computed.marginTop),
+ paraSpaceAfter: pxToPoints(computed.marginBottom),
+ // PptxGenJS margin array is [left, right, bottom, top] (not [top, right, bottom, left] as documented)
+ margin: [
+ pxToPoints(computed.paddingLeft),
+ pxToPoints(computed.paddingRight),
+ pxToPoints(computed.paddingBottom),
+ pxToPoints(computed.paddingTop)
+ ]
+ };
+
+ const transparency = extractAlpha(computed.color);
+ if (transparency !== null) baseStyle.transparency = transparency;
+
+ if (rotation !== null) baseStyle.rotate = rotation;
+
+ const hasFormatting = el.querySelector('b, i, u, strong, em, span, br');
+
+ if (hasFormatting) {
+ // Text with inline formatting
+ const transformStr = computed.textTransform;
+ const runs = parseInlineFormatting(el, {}, [], (str) => applyTextTransform(str, transformStr));
+
+ // Adjust lineSpacing based on largest fontSize in runs
+ const adjustedStyle = { ...baseStyle };
+ if (adjustedStyle.lineSpacing) {
+ const maxFontSize = Math.max(
+ adjustedStyle.fontSize,
+ ...runs.map(r => r.options?.fontSize || 0)
+ );
+ if (maxFontSize > adjustedStyle.fontSize) {
+ const lineHeightMultiplier = adjustedStyle.lineSpacing / adjustedStyle.fontSize;
+ adjustedStyle.lineSpacing = maxFontSize * lineHeightMultiplier;
+ }
+ }
+
+ elements.push({
+ type: el.tagName.toLowerCase(),
+ text: runs,
+ position: { x: pxToInch(x), y: pxToInch(y), w: pxToInch(w), h: pxToInch(h) },
+ style: adjustedStyle
+ });
+ } else {
+ // Plain text - inherit CSS formatting
+ const textTransform = computed.textTransform;
+ const transformedText = applyTextTransform(text, textTransform);
+
+ const isBold = computed.fontWeight === 'bold' || parseInt(computed.fontWeight) >= 600;
+
+ elements.push({
+ type: el.tagName.toLowerCase(),
+ text: transformedText,
+ position: { x: pxToInch(x), y: pxToInch(y), w: pxToInch(w), h: pxToInch(h) },
+ style: {
+ ...baseStyle,
+ bold: isBold && !shouldSkipBold(computed.fontFamily),
+ italic: computed.fontStyle === 'italic',
+ underline: computed.textDecoration.includes('underline')
+ }
+ });
+ }
+
+ processed.add(el);
+ });
+
+ return { background, elements, placeholders, errors };
+ });
+}
+
+async function html2pptx(htmlFile, pres, options = {}) {
+ const {
+ tmpDir = process.env.TMPDIR || '/tmp',
+ slide = null
+ } = options;
+
+ try {
+ // Use Chrome on macOS, default Chromium on Unix
+ const launchOptions = { env: { TMPDIR: tmpDir } };
+ if (process.platform === 'darwin') {
+ launchOptions.channel = 'chrome';
+ }
+
+ const browser = await chromium.launch(launchOptions);
+
+ let bodyDimensions;
+ let slideData;
+
+ const filePath = path.isAbsolute(htmlFile) ? htmlFile : path.join(process.cwd(), htmlFile);
+ const validationErrors = [];
+
+ try {
+ const page = await browser.newPage();
+ page.on('console', (msg) => {
+ // Log the message text to your test runner's console
+ console.log(`Browser console: ${msg.text()}`);
+ });
+
+ await page.goto(`file://${filePath}`);
+
+ bodyDimensions = await getBodyDimensions(page);
+
+ await page.setViewportSize({
+ width: Math.round(bodyDimensions.width),
+ height: Math.round(bodyDimensions.height)
+ });
+
+ slideData = await extractSlideData(page);
+ } finally {
+ await browser.close();
+ }
+
+ // Collect all validation errors
+ if (bodyDimensions.errors && bodyDimensions.errors.length > 0) {
+ validationErrors.push(...bodyDimensions.errors);
+ }
+
+ const dimensionErrors = validateDimensions(bodyDimensions, pres);
+ if (dimensionErrors.length > 0) {
+ validationErrors.push(...dimensionErrors);
+ }
+
+ const textBoxPositionErrors = validateTextBoxPosition(slideData, bodyDimensions);
+ if (textBoxPositionErrors.length > 0) {
+ validationErrors.push(...textBoxPositionErrors);
+ }
+
+ if (slideData.errors && slideData.errors.length > 0) {
+ validationErrors.push(...slideData.errors);
+ }
+
+ // Throw all errors at once if any exist
+ if (validationErrors.length > 0) {
+ const errorMessage = validationErrors.length === 1
+ ? validationErrors[0]
+ : `Multiple validation errors found:\n${validationErrors.map((e, i) => ` ${i + 1}. ${e}`).join('\n')}`;
+ throw new Error(errorMessage);
+ }
+
+ const targetSlide = slide || pres.addSlide();
+
+ await addBackground(slideData, targetSlide, tmpDir);
+ addElements(slideData, targetSlide, pres);
+
+ return { slide: targetSlide, placeholders: slideData.placeholders };
+ } catch (error) {
+ if (!error.message.startsWith(htmlFile)) {
+ throw new Error(`${htmlFile}: ${error.message}`);
+ }
+ throw error;
+ }
+}
+
+module.exports = html2pptx;
\ No newline at end of file
diff --git a/scientific-skills/document-skills/pptx/scripts/inventory.py b/scientific-skills/document-skills/pptx/scripts/inventory.py
new file mode 100755
index 0000000..edda390
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/scripts/inventory.py
@@ -0,0 +1,1020 @@
+#!/usr/bin/env python3
+"""
+Extract structured text content from PowerPoint presentations.
+
+This module provides functionality to:
+- Extract all text content from PowerPoint shapes
+- Preserve paragraph formatting (alignment, bullets, fonts, spacing)
+- Handle nested GroupShapes recursively with correct absolute positions
+- Sort shapes by visual position on slides
+- Filter out slide numbers and non-content placeholders
+- Export to JSON with clean, structured data
+
+Classes:
+ ParagraphData: Represents a text paragraph with formatting
+ ShapeData: Represents a shape with position and text content
+
+Main Functions:
+ extract_text_inventory: Extract all text from a presentation
+ save_inventory: Save extracted data to JSON
+
+Usage:
+ python inventory.py input.pptx output.json
+"""
+
+import argparse
+import json
+import platform
+import sys
+from dataclasses import dataclass
+from pathlib import Path
+from typing import Any, Dict, List, Optional, Tuple, Union
+
+from PIL import Image, ImageDraw, ImageFont
+from pptx import Presentation
+from pptx.enum.text import PP_ALIGN
+from pptx.shapes.base import BaseShape
+
+# Type aliases for cleaner signatures
+JsonValue = Union[str, int, float, bool, None]
+ParagraphDict = Dict[str, JsonValue]
+ShapeDict = Dict[
+ str, Union[str, float, bool, List[ParagraphDict], List[str], Dict[str, Any], None]
+]
+InventoryData = Dict[
+ str, Dict[str, "ShapeData"]
+] # Dict of slide_id -> {shape_id -> ShapeData}
+InventoryDict = Dict[str, Dict[str, ShapeDict]] # JSON-serializable inventory
+
+
+def main():
+ """Main entry point for command-line usage."""
+ parser = argparse.ArgumentParser(
+ description="Extract text inventory from PowerPoint with proper GroupShape support.",
+ formatter_class=argparse.RawDescriptionHelpFormatter,
+ epilog="""
+Examples:
+ python inventory.py presentation.pptx inventory.json
+ Extracts text inventory with correct absolute positions for grouped shapes
+
+ python inventory.py presentation.pptx inventory.json --issues-only
+ Extracts only text shapes that have overflow or overlap issues
+
+The output JSON includes:
+ - All text content organized by slide and shape
+ - Correct absolute positions for shapes in groups
+ - Visual position and size in inches
+ - Paragraph properties and formatting
+ - Issue detection: text overflow and shape overlaps
+ """,
+ )
+
+ parser.add_argument("input", help="Input PowerPoint file (.pptx)")
+ parser.add_argument("output", help="Output JSON file for inventory")
+ parser.add_argument(
+ "--issues-only",
+ action="store_true",
+ help="Include only text shapes that have overflow or overlap issues",
+ )
+
+ args = parser.parse_args()
+
+ input_path = Path(args.input)
+ if not input_path.exists():
+ print(f"Error: Input file not found: {args.input}")
+ sys.exit(1)
+
+ if not input_path.suffix.lower() == ".pptx":
+ print("Error: Input must be a PowerPoint file (.pptx)")
+ sys.exit(1)
+
+ try:
+ print(f"Extracting text inventory from: {args.input}")
+ if args.issues_only:
+ print(
+ "Filtering to include only text shapes with issues (overflow/overlap)"
+ )
+ inventory = extract_text_inventory(input_path, issues_only=args.issues_only)
+
+ output_path = Path(args.output)
+ output_path.parent.mkdir(parents=True, exist_ok=True)
+ save_inventory(inventory, output_path)
+
+ print(f"Output saved to: {args.output}")
+
+ # Report statistics
+ total_slides = len(inventory)
+ total_shapes = sum(len(shapes) for shapes in inventory.values())
+ if args.issues_only:
+ if total_shapes > 0:
+ print(
+ f"Found {total_shapes} text elements with issues in {total_slides} slides"
+ )
+ else:
+ print("No issues discovered")
+ else:
+ print(
+ f"Found text in {total_slides} slides with {total_shapes} text elements"
+ )
+
+ except Exception as e:
+ print(f"Error processing presentation: {e}")
+ import traceback
+
+ traceback.print_exc()
+ sys.exit(1)
+
+
+@dataclass
+class ShapeWithPosition:
+ """A shape with its absolute position on the slide."""
+
+ shape: BaseShape
+ absolute_left: int # in EMUs
+ absolute_top: int # in EMUs
+
+
+class ParagraphData:
+ """Data structure for paragraph properties extracted from a PowerPoint paragraph."""
+
+ def __init__(self, paragraph: Any):
+ """Initialize from a PowerPoint paragraph object.
+
+ Args:
+ paragraph: The PowerPoint paragraph object
+ """
+ self.text: str = paragraph.text.strip()
+ self.bullet: bool = False
+ self.level: Optional[int] = None
+ self.alignment: Optional[str] = None
+ self.space_before: Optional[float] = None
+ self.space_after: Optional[float] = None
+ self.font_name: Optional[str] = None
+ self.font_size: Optional[float] = None
+ self.bold: Optional[bool] = None
+ self.italic: Optional[bool] = None
+ self.underline: Optional[bool] = None
+ self.color: Optional[str] = None
+ self.theme_color: Optional[str] = None
+ self.line_spacing: Optional[float] = None
+
+ # Check for bullet formatting
+ if (
+ hasattr(paragraph, "_p")
+ and paragraph._p is not None
+ and paragraph._p.pPr is not None
+ ):
+ pPr = paragraph._p.pPr
+ ns = "{http://schemas.openxmlformats.org/drawingml/2006/main}"
+ if (
+ pPr.find(f"{ns}buChar") is not None
+ or pPr.find(f"{ns}buAutoNum") is not None
+ ):
+ self.bullet = True
+ if hasattr(paragraph, "level"):
+ self.level = paragraph.level
+
+ # Add alignment if not LEFT (default)
+ if hasattr(paragraph, "alignment") and paragraph.alignment is not None:
+ alignment_map = {
+ PP_ALIGN.CENTER: "CENTER",
+ PP_ALIGN.RIGHT: "RIGHT",
+ PP_ALIGN.JUSTIFY: "JUSTIFY",
+ }
+ if paragraph.alignment in alignment_map:
+ self.alignment = alignment_map[paragraph.alignment]
+
+ # Add spacing properties if set
+ if hasattr(paragraph, "space_before") and paragraph.space_before:
+ self.space_before = paragraph.space_before.pt
+ if hasattr(paragraph, "space_after") and paragraph.space_after:
+ self.space_after = paragraph.space_after.pt
+
+ # Extract font properties from first run
+ if paragraph.runs:
+ first_run = paragraph.runs[0]
+ if hasattr(first_run, "font"):
+ font = first_run.font
+ if font.name:
+ self.font_name = font.name
+ if font.size:
+ self.font_size = font.size.pt
+ if font.bold is not None:
+ self.bold = font.bold
+ if font.italic is not None:
+ self.italic = font.italic
+ if font.underline is not None:
+ self.underline = font.underline
+
+ # Handle color - both RGB and theme colors
+ try:
+ # Try RGB color first
+ if font.color.rgb:
+ self.color = str(font.color.rgb)
+ except (AttributeError, TypeError):
+ # Fall back to theme color
+ try:
+ if font.color.theme_color:
+ self.theme_color = font.color.theme_color.name
+ except (AttributeError, TypeError):
+ pass
+
+ # Add line spacing if set
+ if hasattr(paragraph, "line_spacing") and paragraph.line_spacing is not None:
+ if hasattr(paragraph.line_spacing, "pt"):
+ self.line_spacing = round(paragraph.line_spacing.pt, 2)
+ else:
+ # Multiplier - convert to points
+ font_size = self.font_size if self.font_size else 12.0
+ self.line_spacing = round(paragraph.line_spacing * font_size, 2)
+
+ def to_dict(self) -> ParagraphDict:
+ """Convert to dictionary for JSON serialization, excluding None values."""
+ result: ParagraphDict = {"text": self.text}
+
+ # Add optional fields only if they have values
+ if self.bullet:
+ result["bullet"] = self.bullet
+ if self.level is not None:
+ result["level"] = self.level
+ if self.alignment:
+ result["alignment"] = self.alignment
+ if self.space_before is not None:
+ result["space_before"] = self.space_before
+ if self.space_after is not None:
+ result["space_after"] = self.space_after
+ if self.font_name:
+ result["font_name"] = self.font_name
+ if self.font_size is not None:
+ result["font_size"] = self.font_size
+ if self.bold is not None:
+ result["bold"] = self.bold
+ if self.italic is not None:
+ result["italic"] = self.italic
+ if self.underline is not None:
+ result["underline"] = self.underline
+ if self.color:
+ result["color"] = self.color
+ if self.theme_color:
+ result["theme_color"] = self.theme_color
+ if self.line_spacing is not None:
+ result["line_spacing"] = self.line_spacing
+
+ return result
+
+
+class ShapeData:
+ """Data structure for shape properties extracted from a PowerPoint shape."""
+
+ @staticmethod
+ def emu_to_inches(emu: int) -> float:
+ """Convert EMUs (English Metric Units) to inches."""
+ return emu / 914400.0
+
+ @staticmethod
+ def inches_to_pixels(inches: float, dpi: int = 96) -> int:
+ """Convert inches to pixels at given DPI."""
+ return int(inches * dpi)
+
+ @staticmethod
+ def get_font_path(font_name: str) -> Optional[str]:
+ """Get the font file path for a given font name.
+
+ Args:
+ font_name: Name of the font (e.g., 'Arial', 'Calibri')
+
+ Returns:
+ Path to the font file, or None if not found
+ """
+ system = platform.system()
+
+ # Common font file variations to try
+ font_variations = [
+ font_name,
+ font_name.lower(),
+ font_name.replace(" ", ""),
+ font_name.replace(" ", "-"),
+ ]
+
+ # Define font directories and extensions by platform
+ if system == "Darwin": # macOS
+ font_dirs = [
+ "/System/Library/Fonts/",
+ "/Library/Fonts/",
+ "~/Library/Fonts/",
+ ]
+ extensions = [".ttf", ".otf", ".ttc", ".dfont"]
+ else: # Linux
+ font_dirs = [
+ "/usr/share/fonts/truetype/",
+ "/usr/local/share/fonts/",
+ "~/.fonts/",
+ ]
+ extensions = [".ttf", ".otf"]
+
+ # Try to find the font file
+ from pathlib import Path
+
+ for font_dir in font_dirs:
+ font_dir_path = Path(font_dir).expanduser()
+ if not font_dir_path.exists():
+ continue
+
+ # First try exact matches
+ for variant in font_variations:
+ for ext in extensions:
+ font_path = font_dir_path / f"{variant}{ext}"
+ if font_path.exists():
+ return str(font_path)
+
+ # Then try fuzzy matching - find files containing the font name
+ try:
+ for file_path in font_dir_path.iterdir():
+ if file_path.is_file():
+ file_name_lower = file_path.name.lower()
+ font_name_lower = font_name.lower().replace(" ", "")
+ if font_name_lower in file_name_lower and any(
+ file_name_lower.endswith(ext) for ext in extensions
+ ):
+ return str(file_path)
+ except (OSError, PermissionError):
+ continue
+
+ return None
+
+ @staticmethod
+ def get_slide_dimensions(slide: Any) -> tuple[Optional[int], Optional[int]]:
+ """Get slide dimensions from slide object.
+
+ Args:
+ slide: Slide object
+
+ Returns:
+ Tuple of (width_emu, height_emu) or (None, None) if not found
+ """
+ try:
+ prs = slide.part.package.presentation_part.presentation
+ return prs.slide_width, prs.slide_height
+ except (AttributeError, TypeError):
+ return None, None
+
+ @staticmethod
+ def get_default_font_size(shape: BaseShape, slide_layout: Any) -> Optional[float]:
+ """Extract default font size from slide layout for a placeholder shape.
+
+ Args:
+ shape: Placeholder shape
+ slide_layout: Slide layout containing the placeholder definition
+
+ Returns:
+ Default font size in points, or None if not found
+ """
+ try:
+ if not hasattr(shape, "placeholder_format"):
+ return None
+
+ shape_type = shape.placeholder_format.type # type: ignore
+ for layout_placeholder in slide_layout.placeholders:
+ if layout_placeholder.placeholder_format.type == shape_type:
+ # Find first defRPr element with sz (size) attribute
+ for elem in layout_placeholder.element.iter():
+ if "defRPr" in elem.tag and (sz := elem.get("sz")):
+ return float(sz) / 100.0 # Convert EMUs to points
+ break
+ except Exception:
+ pass
+ return None
+
+ def __init__(
+ self,
+ shape: BaseShape,
+ absolute_left: Optional[int] = None,
+ absolute_top: Optional[int] = None,
+ slide: Optional[Any] = None,
+ ):
+ """Initialize from a PowerPoint shape object.
+
+ Args:
+ shape: The PowerPoint shape object (should be pre-validated)
+ absolute_left: Absolute left position in EMUs (for shapes in groups)
+ absolute_top: Absolute top position in EMUs (for shapes in groups)
+ slide: Optional slide object to get dimensions and layout information
+ """
+ self.shape = shape # Store reference to original shape
+ self.shape_id: str = "" # Will be set after sorting
+
+ # Get slide dimensions from slide object
+ self.slide_width_emu, self.slide_height_emu = (
+ self.get_slide_dimensions(slide) if slide else (None, None)
+ )
+
+ # Get placeholder type if applicable
+ self.placeholder_type: Optional[str] = None
+ self.default_font_size: Optional[float] = None
+ if hasattr(shape, "is_placeholder") and shape.is_placeholder: # type: ignore
+ if shape.placeholder_format and shape.placeholder_format.type: # type: ignore
+ self.placeholder_type = (
+ str(shape.placeholder_format.type).split(".")[-1].split(" ")[0] # type: ignore
+ )
+
+ # Get default font size from layout
+ if slide and hasattr(slide, "slide_layout"):
+ self.default_font_size = self.get_default_font_size(
+ shape, slide.slide_layout
+ )
+
+ # Get position information
+ # Use absolute positions if provided (for shapes in groups), otherwise use shape's position
+ left_emu = (
+ absolute_left
+ if absolute_left is not None
+ else (shape.left if hasattr(shape, "left") else 0)
+ )
+ top_emu = (
+ absolute_top
+ if absolute_top is not None
+ else (shape.top if hasattr(shape, "top") else 0)
+ )
+
+ self.left: float = round(self.emu_to_inches(left_emu), 2) # type: ignore
+ self.top: float = round(self.emu_to_inches(top_emu), 2) # type: ignore
+ self.width: float = round(
+ self.emu_to_inches(shape.width if hasattr(shape, "width") else 0),
+ 2, # type: ignore
+ )
+ self.height: float = round(
+ self.emu_to_inches(shape.height if hasattr(shape, "height") else 0),
+ 2, # type: ignore
+ )
+
+ # Store EMU positions for overflow calculations
+ self.left_emu = left_emu
+ self.top_emu = top_emu
+ self.width_emu = shape.width if hasattr(shape, "width") else 0
+ self.height_emu = shape.height if hasattr(shape, "height") else 0
+
+ # Calculate overflow status
+ self.frame_overflow_bottom: Optional[float] = None
+ self.slide_overflow_right: Optional[float] = None
+ self.slide_overflow_bottom: Optional[float] = None
+ self.overlapping_shapes: Dict[
+ str, float
+ ] = {} # Dict of shape_id -> overlap area in sq inches
+ self.warnings: List[str] = []
+ self._estimate_frame_overflow()
+ self._calculate_slide_overflow()
+ self._detect_bullet_issues()
+
+ @property
+ def paragraphs(self) -> List[ParagraphData]:
+ """Calculate paragraphs from the shape's text frame."""
+ if not self.shape or not hasattr(self.shape, "text_frame"):
+ return []
+
+ paragraphs = []
+ for paragraph in self.shape.text_frame.paragraphs: # type: ignore
+ if paragraph.text.strip():
+ paragraphs.append(ParagraphData(paragraph))
+ return paragraphs
+
+ def _get_default_font_size(self) -> int:
+ """Get default font size from theme text styles or use conservative default."""
+ try:
+ if not (
+ hasattr(self.shape, "part") and hasattr(self.shape.part, "slide_layout")
+ ):
+ return 14
+
+ slide_master = self.shape.part.slide_layout.slide_master # type: ignore
+ if not hasattr(slide_master, "element"):
+ return 14
+
+ # Determine theme style based on placeholder type
+ style_name = "bodyStyle" # Default
+ if self.placeholder_type and "TITLE" in self.placeholder_type:
+ style_name = "titleStyle"
+
+ # Find font size in theme styles
+ for child in slide_master.element.iter():
+ tag = child.tag.split("}")[-1] if "}" in child.tag else child.tag
+ if tag == style_name:
+ for elem in child.iter():
+ if "sz" in elem.attrib:
+ return int(elem.attrib["sz"]) // 100
+ except Exception:
+ pass
+
+ return 14 # Conservative default for body text
+
+ def _get_usable_dimensions(self, text_frame) -> Tuple[int, int]:
+ """Get usable width and height in pixels after accounting for margins."""
+ # Default PowerPoint margins in inches
+ margins = {"top": 0.05, "bottom": 0.05, "left": 0.1, "right": 0.1}
+
+ # Override with actual margins if set
+ if hasattr(text_frame, "margin_top") and text_frame.margin_top:
+ margins["top"] = self.emu_to_inches(text_frame.margin_top)
+ if hasattr(text_frame, "margin_bottom") and text_frame.margin_bottom:
+ margins["bottom"] = self.emu_to_inches(text_frame.margin_bottom)
+ if hasattr(text_frame, "margin_left") and text_frame.margin_left:
+ margins["left"] = self.emu_to_inches(text_frame.margin_left)
+ if hasattr(text_frame, "margin_right") and text_frame.margin_right:
+ margins["right"] = self.emu_to_inches(text_frame.margin_right)
+
+ # Calculate usable area
+ usable_width = self.width - margins["left"] - margins["right"]
+ usable_height = self.height - margins["top"] - margins["bottom"]
+
+ # Convert to pixels
+ return (
+ self.inches_to_pixels(usable_width),
+ self.inches_to_pixels(usable_height),
+ )
+
+ def _wrap_text_line(self, line: str, max_width_px: int, draw, font) -> List[str]:
+ """Wrap a single line of text to fit within max_width_px."""
+ if not line:
+ return [""]
+
+ # Use textlength for efficient width calculation
+ if draw.textlength(line, font=font) <= max_width_px:
+ return [line]
+
+ # Need to wrap - split into words
+ wrapped = []
+ words = line.split(" ")
+ current_line = ""
+
+ for word in words:
+ test_line = current_line + (" " if current_line else "") + word
+ if draw.textlength(test_line, font=font) <= max_width_px:
+ current_line = test_line
+ else:
+ if current_line:
+ wrapped.append(current_line)
+ current_line = word
+
+ if current_line:
+ wrapped.append(current_line)
+
+ return wrapped
+
+ def _estimate_frame_overflow(self) -> None:
+ """Estimate if text overflows the shape bounds using PIL text measurement."""
+ if not self.shape or not hasattr(self.shape, "text_frame"):
+ return
+
+ text_frame = self.shape.text_frame # type: ignore
+ if not text_frame or not text_frame.paragraphs:
+ return
+
+ # Get usable dimensions after accounting for margins
+ usable_width_px, usable_height_px = self._get_usable_dimensions(text_frame)
+ if usable_width_px <= 0 or usable_height_px <= 0:
+ return
+
+ # Set up PIL for text measurement
+ dummy_img = Image.new("RGB", (1, 1))
+ draw = ImageDraw.Draw(dummy_img)
+
+ # Get default font size from placeholder or use conservative estimate
+ default_font_size = self._get_default_font_size()
+
+ # Calculate total height of all paragraphs
+ total_height_px = 0
+
+ for para_idx, paragraph in enumerate(text_frame.paragraphs):
+ if not paragraph.text.strip():
+ continue
+
+ para_data = ParagraphData(paragraph)
+
+ # Load font for this paragraph
+ font_name = para_data.font_name or "Arial"
+ font_size = int(para_data.font_size or default_font_size)
+
+ font = None
+ font_path = self.get_font_path(font_name)
+ if font_path:
+ try:
+ font = ImageFont.truetype(font_path, size=font_size)
+ except Exception:
+ font = ImageFont.load_default()
+ else:
+ font = ImageFont.load_default()
+
+ # Wrap all lines in this paragraph
+ all_wrapped_lines = []
+ for line in paragraph.text.split("\n"):
+ wrapped = self._wrap_text_line(line, usable_width_px, draw, font)
+ all_wrapped_lines.extend(wrapped)
+
+ if all_wrapped_lines:
+ # Calculate line height
+ if para_data.line_spacing:
+ # Custom line spacing explicitly set
+ line_height_px = para_data.line_spacing * 96 / 72
+ else:
+ # PowerPoint default single spacing (1.0x font size)
+ line_height_px = font_size * 96 / 72
+
+ # Add space_before (except first paragraph)
+ if para_idx > 0 and para_data.space_before:
+ total_height_px += para_data.space_before * 96 / 72
+
+ # Add paragraph text height
+ total_height_px += len(all_wrapped_lines) * line_height_px
+
+ # Add space_after
+ if para_data.space_after:
+ total_height_px += para_data.space_after * 96 / 72
+
+ # Check for overflow (ignore negligible overflows <= 0.05")
+ if total_height_px > usable_height_px:
+ overflow_px = total_height_px - usable_height_px
+ overflow_inches = round(overflow_px / 96.0, 2)
+ if overflow_inches > 0.05: # Only report significant overflows
+ self.frame_overflow_bottom = overflow_inches
+
+ def _calculate_slide_overflow(self) -> None:
+ """Calculate if shape overflows the slide boundaries."""
+ if self.slide_width_emu is None or self.slide_height_emu is None:
+ return
+
+ # Check right overflow (ignore negligible overflows <= 0.01")
+ right_edge_emu = self.left_emu + self.width_emu
+ if right_edge_emu > self.slide_width_emu:
+ overflow_emu = right_edge_emu - self.slide_width_emu
+ overflow_inches = round(self.emu_to_inches(overflow_emu), 2)
+ if overflow_inches > 0.01: # Only report significant overflows
+ self.slide_overflow_right = overflow_inches
+
+ # Check bottom overflow (ignore negligible overflows <= 0.01")
+ bottom_edge_emu = self.top_emu + self.height_emu
+ if bottom_edge_emu > self.slide_height_emu:
+ overflow_emu = bottom_edge_emu - self.slide_height_emu
+ overflow_inches = round(self.emu_to_inches(overflow_emu), 2)
+ if overflow_inches > 0.01: # Only report significant overflows
+ self.slide_overflow_bottom = overflow_inches
+
+ def _detect_bullet_issues(self) -> None:
+ """Detect bullet point formatting issues in paragraphs."""
+ if not self.shape or not hasattr(self.shape, "text_frame"):
+ return
+
+ text_frame = self.shape.text_frame # type: ignore
+ if not text_frame or not text_frame.paragraphs:
+ return
+
+ # Common bullet symbols that indicate manual bullets
+ bullet_symbols = ["•", "●", "○"]
+
+ for paragraph in text_frame.paragraphs:
+ text = paragraph.text.strip()
+ # Check for manual bullet symbols
+ if text and any(text.startswith(symbol + " ") for symbol in bullet_symbols):
+ self.warnings.append(
+ "manual_bullet_symbol: use proper bullet formatting"
+ )
+ break
+
+ @property
+ def has_any_issues(self) -> bool:
+ """Check if shape has any issues (overflow, overlap, or warnings)."""
+ return (
+ self.frame_overflow_bottom is not None
+ or self.slide_overflow_right is not None
+ or self.slide_overflow_bottom is not None
+ or len(self.overlapping_shapes) > 0
+ or len(self.warnings) > 0
+ )
+
+ def to_dict(self) -> ShapeDict:
+ """Convert to dictionary for JSON serialization."""
+ result: ShapeDict = {
+ "left": self.left,
+ "top": self.top,
+ "width": self.width,
+ "height": self.height,
+ }
+
+ # Add optional fields if present
+ if self.placeholder_type:
+ result["placeholder_type"] = self.placeholder_type
+
+ if self.default_font_size:
+ result["default_font_size"] = self.default_font_size
+
+ # Add overflow information only if there is overflow
+ overflow_data = {}
+
+ # Add frame overflow if present
+ if self.frame_overflow_bottom is not None:
+ overflow_data["frame"] = {"overflow_bottom": self.frame_overflow_bottom}
+
+ # Add slide overflow if present
+ slide_overflow = {}
+ if self.slide_overflow_right is not None:
+ slide_overflow["overflow_right"] = self.slide_overflow_right
+ if self.slide_overflow_bottom is not None:
+ slide_overflow["overflow_bottom"] = self.slide_overflow_bottom
+ if slide_overflow:
+ overflow_data["slide"] = slide_overflow
+
+ # Only add overflow field if there is overflow
+ if overflow_data:
+ result["overflow"] = overflow_data
+
+ # Add overlap field if there are overlapping shapes
+ if self.overlapping_shapes:
+ result["overlap"] = {"overlapping_shapes": self.overlapping_shapes}
+
+ # Add warnings field if there are warnings
+ if self.warnings:
+ result["warnings"] = self.warnings
+
+ # Add paragraphs after placeholder_type
+ result["paragraphs"] = [para.to_dict() for para in self.paragraphs]
+
+ return result
+
+
+def is_valid_shape(shape: BaseShape) -> bool:
+ """Check if a shape contains meaningful text content."""
+ # Must have a text frame with content
+ if not hasattr(shape, "text_frame") or not shape.text_frame: # type: ignore
+ return False
+
+ text = shape.text_frame.text.strip() # type: ignore
+ if not text:
+ return False
+
+ # Skip slide numbers and numeric footers
+ if hasattr(shape, "is_placeholder") and shape.is_placeholder: # type: ignore
+ if shape.placeholder_format and shape.placeholder_format.type: # type: ignore
+ placeholder_type = (
+ str(shape.placeholder_format.type).split(".")[-1].split(" ")[0] # type: ignore
+ )
+ if placeholder_type == "SLIDE_NUMBER":
+ return False
+ if placeholder_type == "FOOTER" and text.isdigit():
+ return False
+
+ return True
+
+
+def collect_shapes_with_absolute_positions(
+ shape: BaseShape, parent_left: int = 0, parent_top: int = 0
+) -> List[ShapeWithPosition]:
+ """Recursively collect all shapes with valid text, calculating absolute positions.
+
+ For shapes within groups, their positions are relative to the group.
+ This function calculates the absolute position on the slide by accumulating
+ parent group offsets.
+
+ Args:
+ shape: The shape to process
+ parent_left: Accumulated left offset from parent groups (in EMUs)
+ parent_top: Accumulated top offset from parent groups (in EMUs)
+
+ Returns:
+ List of ShapeWithPosition objects with absolute positions
+ """
+ if hasattr(shape, "shapes"): # GroupShape
+ result = []
+ # Get this group's position
+ group_left = shape.left if hasattr(shape, "left") else 0
+ group_top = shape.top if hasattr(shape, "top") else 0
+
+ # Calculate absolute position for this group
+ abs_group_left = parent_left + group_left
+ abs_group_top = parent_top + group_top
+
+ # Process children with accumulated offsets
+ for child in shape.shapes: # type: ignore
+ result.extend(
+ collect_shapes_with_absolute_positions(
+ child, abs_group_left, abs_group_top
+ )
+ )
+ return result
+
+ # Regular shape - check if it has valid text
+ if is_valid_shape(shape):
+ # Calculate absolute position
+ shape_left = shape.left if hasattr(shape, "left") else 0
+ shape_top = shape.top if hasattr(shape, "top") else 0
+
+ return [
+ ShapeWithPosition(
+ shape=shape,
+ absolute_left=parent_left + shape_left,
+ absolute_top=parent_top + shape_top,
+ )
+ ]
+
+ return []
+
+
+def sort_shapes_by_position(shapes: List[ShapeData]) -> List[ShapeData]:
+ """Sort shapes by visual position (top-to-bottom, left-to-right).
+
+ Shapes within 0.5 inches vertically are considered on the same row.
+ """
+ if not shapes:
+ return shapes
+
+ # Sort by top position first
+ shapes = sorted(shapes, key=lambda s: (s.top, s.left))
+
+ # Group shapes by row (within 0.5 inches vertically)
+ result = []
+ row = [shapes[0]]
+ row_top = shapes[0].top
+
+ for shape in shapes[1:]:
+ if abs(shape.top - row_top) <= 0.5:
+ row.append(shape)
+ else:
+ # Sort current row by left position and add to result
+ result.extend(sorted(row, key=lambda s: s.left))
+ row = [shape]
+ row_top = shape.top
+
+ # Don't forget the last row
+ result.extend(sorted(row, key=lambda s: s.left))
+ return result
+
+
+def calculate_overlap(
+ rect1: Tuple[float, float, float, float],
+ rect2: Tuple[float, float, float, float],
+ tolerance: float = 0.05,
+) -> Tuple[bool, float]:
+ """Calculate if and how much two rectangles overlap.
+
+ Args:
+ rect1: (left, top, width, height) of first rectangle in inches
+ rect2: (left, top, width, height) of second rectangle in inches
+ tolerance: Minimum overlap in inches to consider as overlapping (default: 0.05")
+
+ Returns:
+ Tuple of (overlaps, overlap_area) where:
+ - overlaps: True if rectangles overlap by more than tolerance
+ - overlap_area: Area of overlap in square inches
+ """
+ left1, top1, w1, h1 = rect1
+ left2, top2, w2, h2 = rect2
+
+ # Calculate overlap dimensions
+ overlap_width = min(left1 + w1, left2 + w2) - max(left1, left2)
+ overlap_height = min(top1 + h1, top2 + h2) - max(top1, top2)
+
+ # Check if there's meaningful overlap (more than tolerance)
+ if overlap_width > tolerance and overlap_height > tolerance:
+ # Calculate overlap area in square inches
+ overlap_area = overlap_width * overlap_height
+ return True, round(overlap_area, 2)
+
+ return False, 0
+
+
+def detect_overlaps(shapes: List[ShapeData]) -> None:
+ """Detect overlapping shapes and update their overlapping_shapes dictionaries.
+
+ This function requires each ShapeData to have its shape_id already set.
+ It modifies the shapes in-place, adding shape IDs with overlap areas in square inches.
+
+ Args:
+ shapes: List of ShapeData objects with shape_id attributes set
+ """
+ n = len(shapes)
+
+ # Compare each pair of shapes
+ for i in range(n):
+ for j in range(i + 1, n):
+ shape1 = shapes[i]
+ shape2 = shapes[j]
+
+ # Ensure shape IDs are set
+ assert shape1.shape_id, f"Shape at index {i} has no shape_id"
+ assert shape2.shape_id, f"Shape at index {j} has no shape_id"
+
+ rect1 = (shape1.left, shape1.top, shape1.width, shape1.height)
+ rect2 = (shape2.left, shape2.top, shape2.width, shape2.height)
+
+ overlaps, overlap_area = calculate_overlap(rect1, rect2)
+
+ if overlaps:
+ # Add shape IDs with overlap area in square inches
+ shape1.overlapping_shapes[shape2.shape_id] = overlap_area
+ shape2.overlapping_shapes[shape1.shape_id] = overlap_area
+
+
+def extract_text_inventory(
+ pptx_path: Path, prs: Optional[Any] = None, issues_only: bool = False
+) -> InventoryData:
+ """Extract text content from all slides in a PowerPoint presentation.
+
+ Args:
+ pptx_path: Path to the PowerPoint file
+ prs: Optional Presentation object to use. If not provided, will load from pptx_path.
+ issues_only: If True, only include shapes that have overflow or overlap issues
+
+ Returns a nested dictionary: {slide-N: {shape-N: ShapeData}}
+ Shapes are sorted by visual position (top-to-bottom, left-to-right).
+ The ShapeData objects contain the full shape information and can be
+ converted to dictionaries for JSON serialization using to_dict().
+ """
+ if prs is None:
+ prs = Presentation(str(pptx_path))
+ inventory: InventoryData = {}
+
+ for slide_idx, slide in enumerate(prs.slides):
+ # Collect all valid shapes from this slide with absolute positions
+ shapes_with_positions = []
+ for shape in slide.shapes: # type: ignore
+ shapes_with_positions.extend(collect_shapes_with_absolute_positions(shape))
+
+ if not shapes_with_positions:
+ continue
+
+ # Convert to ShapeData with absolute positions and slide reference
+ shape_data_list = [
+ ShapeData(
+ swp.shape,
+ swp.absolute_left,
+ swp.absolute_top,
+ slide,
+ )
+ for swp in shapes_with_positions
+ ]
+
+ # Sort by visual position and assign stable IDs in one step
+ sorted_shapes = sort_shapes_by_position(shape_data_list)
+ for idx, shape_data in enumerate(sorted_shapes):
+ shape_data.shape_id = f"shape-{idx}"
+
+ # Detect overlaps using the stable shape IDs
+ if len(sorted_shapes) > 1:
+ detect_overlaps(sorted_shapes)
+
+ # Filter for issues only if requested (after overlap detection)
+ if issues_only:
+ sorted_shapes = [sd for sd in sorted_shapes if sd.has_any_issues]
+
+ if not sorted_shapes:
+ continue
+
+ # Create slide inventory using the stable shape IDs
+ inventory[f"slide-{slide_idx}"] = {
+ shape_data.shape_id: shape_data for shape_data in sorted_shapes
+ }
+
+ return inventory
+
+
+def get_inventory_as_dict(pptx_path: Path, issues_only: bool = False) -> InventoryDict:
+ """Extract text inventory and return as JSON-serializable dictionaries.
+
+ This is a convenience wrapper around extract_text_inventory that returns
+ dictionaries instead of ShapeData objects, useful for testing and direct
+ JSON serialization.
+
+ Args:
+ pptx_path: Path to the PowerPoint file
+ issues_only: If True, only include shapes that have overflow or overlap issues
+
+ Returns:
+ Nested dictionary with all data serialized for JSON
+ """
+ inventory = extract_text_inventory(pptx_path, issues_only=issues_only)
+
+ # Convert ShapeData objects to dictionaries
+ dict_inventory: InventoryDict = {}
+ for slide_key, shapes in inventory.items():
+ dict_inventory[slide_key] = {
+ shape_key: shape_data.to_dict() for shape_key, shape_data in shapes.items()
+ }
+
+ return dict_inventory
+
+
+def save_inventory(inventory: InventoryData, output_path: Path) -> None:
+ """Save inventory to JSON file with proper formatting.
+
+ Converts ShapeData objects to dictionaries for JSON serialization.
+ """
+ # Convert ShapeData objects to dictionaries
+ json_inventory: InventoryDict = {}
+ for slide_key, shapes in inventory.items():
+ json_inventory[slide_key] = {
+ shape_key: shape_data.to_dict() for shape_key, shape_data in shapes.items()
+ }
+
+ with open(output_path, "w", encoding="utf-8") as f:
+ json.dump(json_inventory, f, indent=2, ensure_ascii=False)
+
+
+if __name__ == "__main__":
+ main()
diff --git a/scientific-skills/document-skills/pptx/scripts/rearrange.py b/scientific-skills/document-skills/pptx/scripts/rearrange.py
new file mode 100755
index 0000000..2519911
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/scripts/rearrange.py
@@ -0,0 +1,231 @@
+#!/usr/bin/env python3
+"""
+Rearrange PowerPoint slides based on a sequence of indices.
+
+Usage:
+ python rearrange.py template.pptx output.pptx 0,34,34,50,52
+
+This will create output.pptx using slides from template.pptx in the specified order.
+Slides can be repeated (e.g., 34 appears twice).
+"""
+
+import argparse
+import shutil
+import sys
+from copy import deepcopy
+from pathlib import Path
+
+import six
+from pptx import Presentation
+
+
+def main():
+ parser = argparse.ArgumentParser(
+ description="Rearrange PowerPoint slides based on a sequence of indices.",
+ formatter_class=argparse.RawDescriptionHelpFormatter,
+ epilog="""
+Examples:
+ python rearrange.py template.pptx output.pptx 0,34,34,50,52
+ Creates output.pptx using slides 0, 34 (twice), 50, and 52 from template.pptx
+
+ python rearrange.py template.pptx output.pptx 5,3,1,2,4
+ Creates output.pptx with slides reordered as specified
+
+Note: Slide indices are 0-based (first slide is 0, second is 1, etc.)
+ """,
+ )
+
+ parser.add_argument("template", help="Path to template PPTX file")
+ parser.add_argument("output", help="Path for output PPTX file")
+ parser.add_argument(
+ "sequence", help="Comma-separated sequence of slide indices (0-based)"
+ )
+
+ args = parser.parse_args()
+
+ # Parse the slide sequence
+ try:
+ slide_sequence = [int(x.strip()) for x in args.sequence.split(",")]
+ except ValueError:
+ print(
+ "Error: Invalid sequence format. Use comma-separated integers (e.g., 0,34,34,50,52)"
+ )
+ sys.exit(1)
+
+ # Check template exists
+ template_path = Path(args.template)
+ if not template_path.exists():
+ print(f"Error: Template file not found: {args.template}")
+ sys.exit(1)
+
+ # Create output directory if needed
+ output_path = Path(args.output)
+ output_path.parent.mkdir(parents=True, exist_ok=True)
+
+ try:
+ rearrange_presentation(template_path, output_path, slide_sequence)
+ except ValueError as e:
+ print(f"Error: {e}")
+ sys.exit(1)
+ except Exception as e:
+ print(f"Error processing presentation: {e}")
+ sys.exit(1)
+
+
+def duplicate_slide(pres, index):
+ """Duplicate a slide in the presentation."""
+ source = pres.slides[index]
+
+ # Use source's layout to preserve formatting
+ new_slide = pres.slides.add_slide(source.slide_layout)
+
+ # Collect all image and media relationships from the source slide
+ image_rels = {}
+ for rel_id, rel in six.iteritems(source.part.rels):
+ if "image" in rel.reltype or "media" in rel.reltype:
+ image_rels[rel_id] = rel
+
+ # CRITICAL: Clear placeholder shapes to avoid duplicates
+ for shape in new_slide.shapes:
+ sp = shape.element
+ sp.getparent().remove(sp)
+
+ # Copy all shapes from source
+ for shape in source.shapes:
+ el = shape.element
+ new_el = deepcopy(el)
+ new_slide.shapes._spTree.insert_element_before(new_el, "p:extLst")
+
+ # Handle picture shapes - need to update the blip reference
+ # Look for all blip elements (they can be in pic or other contexts)
+ # Using the element's own xpath method without namespaces argument
+ blips = new_el.xpath(".//a:blip[@r:embed]")
+ for blip in blips:
+ old_rId = blip.get(
+ "{http://schemas.openxmlformats.org/officeDocument/2006/relationships}embed"
+ )
+ if old_rId in image_rels:
+ # Create a new relationship in the destination slide for this image
+ old_rel = image_rels[old_rId]
+ # get_or_add returns the rId directly, or adds and returns new rId
+ new_rId = new_slide.part.rels.get_or_add(
+ old_rel.reltype, old_rel._target
+ )
+ # Update the blip's embed reference to use the new relationship ID
+ blip.set(
+ "{http://schemas.openxmlformats.org/officeDocument/2006/relationships}embed",
+ new_rId,
+ )
+
+ # Copy any additional image/media relationships that might be referenced elsewhere
+ for rel_id, rel in image_rels.items():
+ try:
+ new_slide.part.rels.get_or_add(rel.reltype, rel._target)
+ except Exception:
+ pass # Relationship might already exist
+
+ return new_slide
+
+
+def delete_slide(pres, index):
+ """Delete a slide from the presentation."""
+ rId = pres.slides._sldIdLst[index].rId
+ pres.part.drop_rel(rId)
+ del pres.slides._sldIdLst[index]
+
+
+def reorder_slides(pres, slide_index, target_index):
+ """Move a slide from one position to another."""
+ slides = pres.slides._sldIdLst
+
+ # Remove slide element from current position
+ slide_element = slides[slide_index]
+ slides.remove(slide_element)
+
+ # Insert at target position
+ slides.insert(target_index, slide_element)
+
+
+def rearrange_presentation(template_path, output_path, slide_sequence):
+ """
+ Create a new presentation with slides from template in specified order.
+
+ Args:
+ template_path: Path to template PPTX file
+ output_path: Path for output PPTX file
+ slide_sequence: List of slide indices (0-based) to include
+ """
+ # Copy template to preserve dimensions and theme
+ if template_path != output_path:
+ shutil.copy2(template_path, output_path)
+ prs = Presentation(output_path)
+ else:
+ prs = Presentation(template_path)
+
+ total_slides = len(prs.slides)
+
+ # Validate indices
+ for idx in slide_sequence:
+ if idx < 0 or idx >= total_slides:
+ raise ValueError(f"Slide index {idx} out of range (0-{total_slides - 1})")
+
+ # Track original slides and their duplicates
+ slide_map = [] # List of actual slide indices for final presentation
+ duplicated = {} # Track duplicates: original_idx -> [duplicate_indices]
+
+ # Step 1: DUPLICATE repeated slides
+ print(f"Processing {len(slide_sequence)} slides from template...")
+ for i, template_idx in enumerate(slide_sequence):
+ if template_idx in duplicated and duplicated[template_idx]:
+ # Already duplicated this slide, use the duplicate
+ slide_map.append(duplicated[template_idx].pop(0))
+ print(f" [{i}] Using duplicate of slide {template_idx}")
+ elif slide_sequence.count(template_idx) > 1 and template_idx not in duplicated:
+ # First occurrence of a repeated slide - create duplicates
+ slide_map.append(template_idx)
+ duplicates = []
+ count = slide_sequence.count(template_idx) - 1
+ print(
+ f" [{i}] Using original slide {template_idx}, creating {count} duplicate(s)"
+ )
+ for _ in range(count):
+ duplicate_slide(prs, template_idx)
+ duplicates.append(len(prs.slides) - 1)
+ duplicated[template_idx] = duplicates
+ else:
+ # Unique slide or first occurrence already handled, use original
+ slide_map.append(template_idx)
+ print(f" [{i}] Using original slide {template_idx}")
+
+ # Step 2: DELETE unwanted slides (work backwards)
+ slides_to_keep = set(slide_map)
+ print(f"\nDeleting {len(prs.slides) - len(slides_to_keep)} unused slides...")
+ for i in range(len(prs.slides) - 1, -1, -1):
+ if i not in slides_to_keep:
+ delete_slide(prs, i)
+ # Update slide_map indices after deletion
+ slide_map = [idx - 1 if idx > i else idx for idx in slide_map]
+
+ # Step 3: REORDER to final sequence
+ print(f"Reordering {len(slide_map)} slides to final sequence...")
+ for target_pos in range(len(slide_map)):
+ # Find which slide should be at target_pos
+ current_pos = slide_map[target_pos]
+ if current_pos != target_pos:
+ reorder_slides(prs, current_pos, target_pos)
+ # Update slide_map: the move shifts other slides
+ for i in range(len(slide_map)):
+ if slide_map[i] > current_pos and slide_map[i] <= target_pos:
+ slide_map[i] -= 1
+ elif slide_map[i] < current_pos and slide_map[i] >= target_pos:
+ slide_map[i] += 1
+ slide_map[target_pos] = target_pos
+
+ # Save the presentation
+ prs.save(output_path)
+ print(f"\nSaved rearranged presentation to: {output_path}")
+ print(f"Final presentation has {len(prs.slides)} slides")
+
+
+if __name__ == "__main__":
+ main()
diff --git a/scientific-skills/document-skills/pptx/scripts/replace.py b/scientific-skills/document-skills/pptx/scripts/replace.py
new file mode 100755
index 0000000..8f7a8b1
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/scripts/replace.py
@@ -0,0 +1,385 @@
+#!/usr/bin/env python3
+"""Apply text replacements to PowerPoint presentation.
+
+Usage:
+ python replace.py
+
+The replacements JSON should have the structure output by inventory.py.
+ALL text shapes identified by inventory.py will have their text cleared
+unless "paragraphs" is specified in the replacements for that shape.
+"""
+
+import json
+import sys
+from pathlib import Path
+from typing import Any, Dict, List
+
+from inventory import InventoryData, extract_text_inventory
+from pptx import Presentation
+from pptx.dml.color import RGBColor
+from pptx.enum.dml import MSO_THEME_COLOR
+from pptx.enum.text import PP_ALIGN
+from pptx.oxml.xmlchemy import OxmlElement
+from pptx.util import Pt
+
+
+def clear_paragraph_bullets(paragraph):
+ """Clear bullet formatting from a paragraph."""
+ pPr = paragraph._element.get_or_add_pPr()
+
+ # Remove existing bullet elements
+ for child in list(pPr):
+ if (
+ child.tag.endswith("buChar")
+ or child.tag.endswith("buNone")
+ or child.tag.endswith("buAutoNum")
+ or child.tag.endswith("buFont")
+ ):
+ pPr.remove(child)
+
+ return pPr
+
+
+def apply_paragraph_properties(paragraph, para_data: Dict[str, Any]):
+ """Apply formatting properties to a paragraph."""
+ # Get the text but don't set it on paragraph directly yet
+ text = para_data.get("text", "")
+
+ # Get or create paragraph properties
+ pPr = clear_paragraph_bullets(paragraph)
+
+ # Handle bullet formatting
+ if para_data.get("bullet", False):
+ level = para_data.get("level", 0)
+ paragraph.level = level
+
+ # Calculate font-proportional indentation
+ font_size = para_data.get("font_size", 18.0)
+ level_indent_emu = int((font_size * (1.6 + level * 1.6)) * 12700)
+ hanging_indent_emu = int(-font_size * 0.8 * 12700)
+
+ # Set indentation
+ pPr.attrib["marL"] = str(level_indent_emu)
+ pPr.attrib["indent"] = str(hanging_indent_emu)
+
+ # Add bullet character
+ buChar = OxmlElement("a:buChar")
+ buChar.set("char", "•")
+ pPr.append(buChar)
+
+ # Default to left alignment for bullets if not specified
+ if "alignment" not in para_data:
+ paragraph.alignment = PP_ALIGN.LEFT
+ else:
+ # Remove indentation for non-bullet text
+ pPr.attrib["marL"] = "0"
+ pPr.attrib["indent"] = "0"
+
+ # Add buNone element
+ buNone = OxmlElement("a:buNone")
+ pPr.insert(0, buNone)
+
+ # Apply alignment
+ if "alignment" in para_data:
+ alignment_map = {
+ "LEFT": PP_ALIGN.LEFT,
+ "CENTER": PP_ALIGN.CENTER,
+ "RIGHT": PP_ALIGN.RIGHT,
+ "JUSTIFY": PP_ALIGN.JUSTIFY,
+ }
+ if para_data["alignment"] in alignment_map:
+ paragraph.alignment = alignment_map[para_data["alignment"]]
+
+ # Apply spacing
+ if "space_before" in para_data:
+ paragraph.space_before = Pt(para_data["space_before"])
+ if "space_after" in para_data:
+ paragraph.space_after = Pt(para_data["space_after"])
+ if "line_spacing" in para_data:
+ paragraph.line_spacing = Pt(para_data["line_spacing"])
+
+ # Apply run-level formatting
+ if not paragraph.runs:
+ run = paragraph.add_run()
+ run.text = text
+ else:
+ run = paragraph.runs[0]
+ run.text = text
+
+ # Apply font properties
+ apply_font_properties(run, para_data)
+
+
+def apply_font_properties(run, para_data: Dict[str, Any]):
+ """Apply font properties to a text run."""
+ if "bold" in para_data:
+ run.font.bold = para_data["bold"]
+ if "italic" in para_data:
+ run.font.italic = para_data["italic"]
+ if "underline" in para_data:
+ run.font.underline = para_data["underline"]
+ if "font_size" in para_data:
+ run.font.size = Pt(para_data["font_size"])
+ if "font_name" in para_data:
+ run.font.name = para_data["font_name"]
+
+ # Apply color - prefer RGB, fall back to theme_color
+ if "color" in para_data:
+ color_hex = para_data["color"].lstrip("#")
+ if len(color_hex) == 6:
+ r = int(color_hex[0:2], 16)
+ g = int(color_hex[2:4], 16)
+ b = int(color_hex[4:6], 16)
+ run.font.color.rgb = RGBColor(r, g, b)
+ elif "theme_color" in para_data:
+ # Get theme color by name (e.g., "DARK_1", "ACCENT_1")
+ theme_name = para_data["theme_color"]
+ try:
+ run.font.color.theme_color = getattr(MSO_THEME_COLOR, theme_name)
+ except AttributeError:
+ print(f" WARNING: Unknown theme color name '{theme_name}'")
+
+
+def detect_frame_overflow(inventory: InventoryData) -> Dict[str, Dict[str, float]]:
+ """Detect text overflow in shapes (text exceeding shape bounds).
+
+ Returns dict of slide_key -> shape_key -> overflow_inches.
+ Only includes shapes that have text overflow.
+ """
+ overflow_map = {}
+
+ for slide_key, shapes_dict in inventory.items():
+ for shape_key, shape_data in shapes_dict.items():
+ # Check for frame overflow (text exceeding shape bounds)
+ if shape_data.frame_overflow_bottom is not None:
+ if slide_key not in overflow_map:
+ overflow_map[slide_key] = {}
+ overflow_map[slide_key][shape_key] = shape_data.frame_overflow_bottom
+
+ return overflow_map
+
+
+def validate_replacements(inventory: InventoryData, replacements: Dict) -> List[str]:
+ """Validate that all shapes in replacements exist in inventory.
+
+ Returns list of error messages.
+ """
+ errors = []
+
+ for slide_key, shapes_data in replacements.items():
+ if not slide_key.startswith("slide-"):
+ continue
+
+ # Check if slide exists
+ if slide_key not in inventory:
+ errors.append(f"Slide '{slide_key}' not found in inventory")
+ continue
+
+ # Check each shape
+ for shape_key in shapes_data.keys():
+ if shape_key not in inventory[slide_key]:
+ # Find shapes without replacements defined and show their content
+ unused_with_content = []
+ for k in inventory[slide_key].keys():
+ if k not in shapes_data:
+ shape_data = inventory[slide_key][k]
+ # Get text from paragraphs as preview
+ paragraphs = shape_data.paragraphs
+ if paragraphs and paragraphs[0].text:
+ first_text = paragraphs[0].text[:50]
+ if len(paragraphs[0].text) > 50:
+ first_text += "..."
+ unused_with_content.append(f"{k} ('{first_text}')")
+ else:
+ unused_with_content.append(k)
+
+ errors.append(
+ f"Shape '{shape_key}' not found on '{slide_key}'. "
+ f"Shapes without replacements: {', '.join(sorted(unused_with_content)) if unused_with_content else 'none'}"
+ )
+
+ return errors
+
+
+def check_duplicate_keys(pairs):
+ """Check for duplicate keys when loading JSON."""
+ result = {}
+ for key, value in pairs:
+ if key in result:
+ raise ValueError(f"Duplicate key found in JSON: '{key}'")
+ result[key] = value
+ return result
+
+
+def apply_replacements(pptx_file: str, json_file: str, output_file: str):
+ """Apply text replacements from JSON to PowerPoint presentation."""
+
+ # Load presentation
+ prs = Presentation(pptx_file)
+
+ # Get inventory of all text shapes (returns ShapeData objects)
+ # Pass prs to use same Presentation instance
+ inventory = extract_text_inventory(Path(pptx_file), prs)
+
+ # Detect text overflow in original presentation
+ original_overflow = detect_frame_overflow(inventory)
+
+ # Load replacement data with duplicate key detection
+ with open(json_file, "r") as f:
+ replacements = json.load(f, object_pairs_hook=check_duplicate_keys)
+
+ # Validate replacements
+ errors = validate_replacements(inventory, replacements)
+ if errors:
+ print("ERROR: Invalid shapes in replacement JSON:")
+ for error in errors:
+ print(f" - {error}")
+ print("\nPlease check the inventory and update your replacement JSON.")
+ print(
+ "You can regenerate the inventory with: python inventory.py "
+ )
+ raise ValueError(f"Found {len(errors)} validation error(s)")
+
+ # Track statistics
+ shapes_processed = 0
+ shapes_cleared = 0
+ shapes_replaced = 0
+
+ # Process each slide from inventory
+ for slide_key, shapes_dict in inventory.items():
+ if not slide_key.startswith("slide-"):
+ continue
+
+ slide_index = int(slide_key.split("-")[1])
+
+ if slide_index >= len(prs.slides):
+ print(f"Warning: Slide {slide_index} not found")
+ continue
+
+ # Process each shape from inventory
+ for shape_key, shape_data in shapes_dict.items():
+ shapes_processed += 1
+
+ # Get the shape directly from ShapeData
+ shape = shape_data.shape
+ if not shape:
+ print(f"Warning: {shape_key} has no shape reference")
+ continue
+
+ # ShapeData already validates text_frame in __init__
+ text_frame = shape.text_frame # type: ignore
+
+ text_frame.clear() # type: ignore
+ shapes_cleared += 1
+
+ # Check for replacement paragraphs
+ replacement_shape_data = replacements.get(slide_key, {}).get(shape_key, {})
+ if "paragraphs" not in replacement_shape_data:
+ continue
+
+ shapes_replaced += 1
+
+ # Add replacement paragraphs
+ for i, para_data in enumerate(replacement_shape_data["paragraphs"]):
+ if i == 0:
+ p = text_frame.paragraphs[0] # type: ignore
+ else:
+ p = text_frame.add_paragraph() # type: ignore
+
+ apply_paragraph_properties(p, para_data)
+
+ # Check for issues after replacements
+ # Save to a temporary file and reload to avoid modifying the presentation during inventory
+ # (extract_text_inventory accesses font.color which adds empty elements)
+ import tempfile
+
+ with tempfile.NamedTemporaryFile(suffix=".pptx", delete=False) as tmp:
+ tmp_path = Path(tmp.name)
+ prs.save(str(tmp_path))
+
+ try:
+ updated_inventory = extract_text_inventory(tmp_path)
+ updated_overflow = detect_frame_overflow(updated_inventory)
+ finally:
+ tmp_path.unlink() # Clean up temp file
+
+ # Check if any text overflow got worse
+ overflow_errors = []
+ for slide_key, shape_overflows in updated_overflow.items():
+ for shape_key, new_overflow in shape_overflows.items():
+ # Get original overflow (0 if there was no overflow before)
+ original = original_overflow.get(slide_key, {}).get(shape_key, 0.0)
+
+ # Error if overflow increased
+ if new_overflow > original + 0.01: # Small tolerance for rounding
+ increase = new_overflow - original
+ overflow_errors.append(
+ f'{slide_key}/{shape_key}: overflow worsened by {increase:.2f}" '
+ f'(was {original:.2f}", now {new_overflow:.2f}")'
+ )
+
+ # Collect warnings from updated shapes
+ warnings = []
+ for slide_key, shapes_dict in updated_inventory.items():
+ for shape_key, shape_data in shapes_dict.items():
+ if shape_data.warnings:
+ for warning in shape_data.warnings:
+ warnings.append(f"{slide_key}/{shape_key}: {warning}")
+
+ # Fail if there are any issues
+ if overflow_errors or warnings:
+ print("\nERROR: Issues detected in replacement output:")
+ if overflow_errors:
+ print("\nText overflow worsened:")
+ for error in overflow_errors:
+ print(f" - {error}")
+ if warnings:
+ print("\nFormatting warnings:")
+ for warning in warnings:
+ print(f" - {warning}")
+ print("\nPlease fix these issues before saving.")
+ raise ValueError(
+ f"Found {len(overflow_errors)} overflow error(s) and {len(warnings)} warning(s)"
+ )
+
+ # Save the presentation
+ prs.save(output_file)
+
+ # Report results
+ print(f"Saved updated presentation to: {output_file}")
+ print(f"Processed {len(prs.slides)} slides")
+ print(f" - Shapes processed: {shapes_processed}")
+ print(f" - Shapes cleared: {shapes_cleared}")
+ print(f" - Shapes replaced: {shapes_replaced}")
+
+
+def main():
+ """Main entry point for command-line usage."""
+ if len(sys.argv) != 4:
+ print(__doc__)
+ sys.exit(1)
+
+ input_pptx = Path(sys.argv[1])
+ replacements_json = Path(sys.argv[2])
+ output_pptx = Path(sys.argv[3])
+
+ if not input_pptx.exists():
+ print(f"Error: Input file '{input_pptx}' not found")
+ sys.exit(1)
+
+ if not replacements_json.exists():
+ print(f"Error: Replacements JSON file '{replacements_json}' not found")
+ sys.exit(1)
+
+ try:
+ apply_replacements(str(input_pptx), str(replacements_json), str(output_pptx))
+ except Exception as e:
+ print(f"Error applying replacements: {e}")
+ import traceback
+
+ traceback.print_exc()
+ sys.exit(1)
+
+
+if __name__ == "__main__":
+ main()
diff --git a/scientific-skills/document-skills/pptx/scripts/thumbnail.py b/scientific-skills/document-skills/pptx/scripts/thumbnail.py
new file mode 100755
index 0000000..5c7fdf1
--- /dev/null
+++ b/scientific-skills/document-skills/pptx/scripts/thumbnail.py
@@ -0,0 +1,450 @@
+#!/usr/bin/env python3
+"""
+Create thumbnail grids from PowerPoint presentation slides.
+
+Creates a grid layout of slide thumbnails with configurable columns (max 6).
+Each grid contains up to cols×(cols+1) images. For presentations with more
+slides, multiple numbered grid files are created automatically.
+
+The program outputs the names of all files created.
+
+Output:
+- Single grid: {prefix}.jpg (if slides fit in one grid)
+- Multiple grids: {prefix}-1.jpg, {prefix}-2.jpg, etc.
+
+Grid limits by column count:
+- 3 cols: max 12 slides per grid (3×4)
+- 4 cols: max 20 slides per grid (4×5)
+- 5 cols: max 30 slides per grid (5×6) [default]
+- 6 cols: max 42 slides per grid (6×7)
+
+Usage:
+ python thumbnail.py input.pptx [output_prefix] [--cols N] [--outline-placeholders]
+
+Examples:
+ python thumbnail.py presentation.pptx
+ # Creates: thumbnails.jpg (using default prefix)
+ # Outputs:
+ # Created 1 grid(s):
+ # - thumbnails.jpg
+
+ python thumbnail.py large-deck.pptx grid --cols 4
+ # Creates: grid-1.jpg, grid-2.jpg, grid-3.jpg
+ # Outputs:
+ # Created 3 grid(s):
+ # - grid-1.jpg
+ # - grid-2.jpg
+ # - grid-3.jpg
+
+ python thumbnail.py template.pptx analysis --outline-placeholders
+ # Creates thumbnail grids with red outlines around text placeholders
+"""
+
+import argparse
+import subprocess
+import sys
+import tempfile
+from pathlib import Path
+
+from inventory import extract_text_inventory
+from PIL import Image, ImageDraw, ImageFont
+from pptx import Presentation
+
+# Constants
+THUMBNAIL_WIDTH = 300 # Fixed thumbnail width in pixels
+CONVERSION_DPI = 100 # DPI for PDF to image conversion
+MAX_COLS = 6 # Maximum number of columns
+DEFAULT_COLS = 5 # Default number of columns
+JPEG_QUALITY = 95 # JPEG compression quality
+
+# Grid layout constants
+GRID_PADDING = 20 # Padding between thumbnails
+BORDER_WIDTH = 2 # Border width around thumbnails
+FONT_SIZE_RATIO = 0.12 # Font size as fraction of thumbnail width
+LABEL_PADDING_RATIO = 0.4 # Label padding as fraction of font size
+
+
+def main():
+ parser = argparse.ArgumentParser(
+ description="Create thumbnail grids from PowerPoint slides."
+ )
+ parser.add_argument("input", help="Input PowerPoint file (.pptx)")
+ parser.add_argument(
+ "output_prefix",
+ nargs="?",
+ default="thumbnails",
+ help="Output prefix for image files (default: thumbnails, will create prefix.jpg or prefix-N.jpg)",
+ )
+ parser.add_argument(
+ "--cols",
+ type=int,
+ default=DEFAULT_COLS,
+ help=f"Number of columns (default: {DEFAULT_COLS}, max: {MAX_COLS})",
+ )
+ parser.add_argument(
+ "--outline-placeholders",
+ action="store_true",
+ help="Outline text placeholders with a colored border",
+ )
+
+ args = parser.parse_args()
+
+ # Validate columns
+ cols = min(args.cols, MAX_COLS)
+ if args.cols > MAX_COLS:
+ print(f"Warning: Columns limited to {MAX_COLS} (requested {args.cols})")
+
+ # Validate input
+ input_path = Path(args.input)
+ if not input_path.exists() or input_path.suffix.lower() != ".pptx":
+ print(f"Error: Invalid PowerPoint file: {args.input}")
+ sys.exit(1)
+
+ # Construct output path (always JPG)
+ output_path = Path(f"{args.output_prefix}.jpg")
+
+ print(f"Processing: {args.input}")
+
+ try:
+ with tempfile.TemporaryDirectory() as temp_dir:
+ # Get placeholder regions if outlining is enabled
+ placeholder_regions = None
+ slide_dimensions = None
+ if args.outline_placeholders:
+ print("Extracting placeholder regions...")
+ placeholder_regions, slide_dimensions = get_placeholder_regions(
+ input_path
+ )
+ if placeholder_regions:
+ print(f"Found placeholders on {len(placeholder_regions)} slides")
+
+ # Convert slides to images
+ slide_images = convert_to_images(input_path, Path(temp_dir), CONVERSION_DPI)
+ if not slide_images:
+ print("Error: No slides found")
+ sys.exit(1)
+
+ print(f"Found {len(slide_images)} slides")
+
+ # Create grids (max cols×(cols+1) images per grid)
+ grid_files = create_grids(
+ slide_images,
+ cols,
+ THUMBNAIL_WIDTH,
+ output_path,
+ placeholder_regions,
+ slide_dimensions,
+ )
+
+ # Print saved files
+ print(f"Created {len(grid_files)} grid(s):")
+ for grid_file in grid_files:
+ print(f" - {grid_file}")
+
+ except Exception as e:
+ print(f"Error: {e}")
+ sys.exit(1)
+
+
+def create_hidden_slide_placeholder(size):
+ """Create placeholder image for hidden slides."""
+ img = Image.new("RGB", size, color="#F0F0F0")
+ draw = ImageDraw.Draw(img)
+ line_width = max(5, min(size) // 100)
+ draw.line([(0, 0), size], fill="#CCCCCC", width=line_width)
+ draw.line([(size[0], 0), (0, size[1])], fill="#CCCCCC", width=line_width)
+ return img
+
+
+def get_placeholder_regions(pptx_path):
+ """Extract ALL text regions from the presentation.
+
+ Returns a tuple of (placeholder_regions, slide_dimensions).
+ text_regions is a dict mapping slide indices to lists of text regions.
+ Each region is a dict with 'left', 'top', 'width', 'height' in inches.
+ slide_dimensions is a tuple of (width_inches, height_inches).
+ """
+ prs = Presentation(str(pptx_path))
+ inventory = extract_text_inventory(pptx_path, prs)
+ placeholder_regions = {}
+
+ # Get actual slide dimensions in inches (EMU to inches conversion)
+ slide_width_inches = (prs.slide_width or 9144000) / 914400.0
+ slide_height_inches = (prs.slide_height or 5143500) / 914400.0
+
+ for slide_key, shapes in inventory.items():
+ # Extract slide index from "slide-N" format
+ slide_idx = int(slide_key.split("-")[1])
+ regions = []
+
+ for shape_key, shape_data in shapes.items():
+ # The inventory only contains shapes with text, so all shapes should be highlighted
+ regions.append(
+ {
+ "left": shape_data.left,
+ "top": shape_data.top,
+ "width": shape_data.width,
+ "height": shape_data.height,
+ }
+ )
+
+ if regions:
+ placeholder_regions[slide_idx] = regions
+
+ return placeholder_regions, (slide_width_inches, slide_height_inches)
+
+
+def convert_to_images(pptx_path, temp_dir, dpi):
+ """Convert PowerPoint to images via PDF, handling hidden slides."""
+ # Detect hidden slides
+ print("Analyzing presentation...")
+ prs = Presentation(str(pptx_path))
+ total_slides = len(prs.slides)
+
+ # Find hidden slides (1-based indexing for display)
+ hidden_slides = {
+ idx + 1
+ for idx, slide in enumerate(prs.slides)
+ if slide.element.get("show") == "0"
+ }
+
+ print(f"Total slides: {total_slides}")
+ if hidden_slides:
+ print(f"Hidden slides: {sorted(hidden_slides)}")
+
+ pdf_path = temp_dir / f"{pptx_path.stem}.pdf"
+
+ # Convert to PDF
+ print("Converting to PDF...")
+ result = subprocess.run(
+ [
+ "soffice",
+ "--headless",
+ "--convert-to",
+ "pdf",
+ "--outdir",
+ str(temp_dir),
+ str(pptx_path),
+ ],
+ capture_output=True,
+ text=True,
+ )
+ if result.returncode != 0 or not pdf_path.exists():
+ raise RuntimeError("PDF conversion failed")
+
+ # Convert PDF to images
+ print(f"Converting to images at {dpi} DPI...")
+ result = subprocess.run(
+ ["pdftoppm", "-jpeg", "-r", str(dpi), str(pdf_path), str(temp_dir / "slide")],
+ capture_output=True,
+ text=True,
+ )
+ if result.returncode != 0:
+ raise RuntimeError("Image conversion failed")
+
+ visible_images = sorted(temp_dir.glob("slide-*.jpg"))
+
+ # Create full list with placeholders for hidden slides
+ all_images = []
+ visible_idx = 0
+
+ # Get placeholder dimensions from first visible slide
+ if visible_images:
+ with Image.open(visible_images[0]) as img:
+ placeholder_size = img.size
+ else:
+ placeholder_size = (1920, 1080)
+
+ for slide_num in range(1, total_slides + 1):
+ if slide_num in hidden_slides:
+ # Create placeholder image for hidden slide
+ placeholder_path = temp_dir / f"hidden-{slide_num:03d}.jpg"
+ placeholder_img = create_hidden_slide_placeholder(placeholder_size)
+ placeholder_img.save(placeholder_path, "JPEG")
+ all_images.append(placeholder_path)
+ else:
+ # Use the actual visible slide image
+ if visible_idx < len(visible_images):
+ all_images.append(visible_images[visible_idx])
+ visible_idx += 1
+
+ return all_images
+
+
+def create_grids(
+ image_paths,
+ cols,
+ width,
+ output_path,
+ placeholder_regions=None,
+ slide_dimensions=None,
+):
+ """Create multiple thumbnail grids from slide images, max cols×(cols+1) images per grid."""
+ # Maximum images per grid is cols × (cols + 1) for better proportions
+ max_images_per_grid = cols * (cols + 1)
+ grid_files = []
+
+ print(
+ f"Creating grids with {cols} columns (max {max_images_per_grid} images per grid)"
+ )
+
+ # Split images into chunks
+ for chunk_idx, start_idx in enumerate(
+ range(0, len(image_paths), max_images_per_grid)
+ ):
+ end_idx = min(start_idx + max_images_per_grid, len(image_paths))
+ chunk_images = image_paths[start_idx:end_idx]
+
+ # Create grid for this chunk
+ grid = create_grid(
+ chunk_images, cols, width, start_idx, placeholder_regions, slide_dimensions
+ )
+
+ # Generate output filename
+ if len(image_paths) <= max_images_per_grid:
+ # Single grid - use base filename without suffix
+ grid_filename = output_path
+ else:
+ # Multiple grids - insert index before extension with dash
+ stem = output_path.stem
+ suffix = output_path.suffix
+ grid_filename = output_path.parent / f"{stem}-{chunk_idx + 1}{suffix}"
+
+ # Save grid
+ grid_filename.parent.mkdir(parents=True, exist_ok=True)
+ grid.save(str(grid_filename), quality=JPEG_QUALITY)
+ grid_files.append(str(grid_filename))
+
+ return grid_files
+
+
+def create_grid(
+ image_paths,
+ cols,
+ width,
+ start_slide_num=0,
+ placeholder_regions=None,
+ slide_dimensions=None,
+):
+ """Create thumbnail grid from slide images with optional placeholder outlining."""
+ font_size = int(width * FONT_SIZE_RATIO)
+ label_padding = int(font_size * LABEL_PADDING_RATIO)
+
+ # Get dimensions
+ with Image.open(image_paths[0]) as img:
+ aspect = img.height / img.width
+ height = int(width * aspect)
+
+ # Calculate grid size
+ rows = (len(image_paths) + cols - 1) // cols
+ grid_w = cols * width + (cols + 1) * GRID_PADDING
+ grid_h = rows * (height + font_size + label_padding * 2) + (rows + 1) * GRID_PADDING
+
+ # Create grid
+ grid = Image.new("RGB", (grid_w, grid_h), "white")
+ draw = ImageDraw.Draw(grid)
+
+ # Load font with size based on thumbnail width
+ try:
+ # Use Pillow's default font with size
+ font = ImageFont.load_default(size=font_size)
+ except Exception:
+ # Fall back to basic default font if size parameter not supported
+ font = ImageFont.load_default()
+
+ # Place thumbnails
+ for i, img_path in enumerate(image_paths):
+ row, col = i // cols, i % cols
+ x = col * width + (col + 1) * GRID_PADDING
+ y_base = (
+ row * (height + font_size + label_padding * 2) + (row + 1) * GRID_PADDING
+ )
+
+ # Add label with actual slide number
+ label = f"{start_slide_num + i}"
+ bbox = draw.textbbox((0, 0), label, font=font)
+ text_w = bbox[2] - bbox[0]
+ draw.text(
+ (x + (width - text_w) // 2, y_base + label_padding),
+ label,
+ fill="black",
+ font=font,
+ )
+
+ # Add thumbnail below label with proportional spacing
+ y_thumbnail = y_base + label_padding + font_size + label_padding
+
+ with Image.open(img_path) as img:
+ # Get original dimensions before thumbnail
+ orig_w, orig_h = img.size
+
+ # Apply placeholder outlines if enabled
+ if placeholder_regions and (start_slide_num + i) in placeholder_regions:
+ # Convert to RGBA for transparency support
+ if img.mode != "RGBA":
+ img = img.convert("RGBA")
+
+ # Get the regions for this slide
+ regions = placeholder_regions[start_slide_num + i]
+
+ # Calculate scale factors using actual slide dimensions
+ if slide_dimensions:
+ slide_width_inches, slide_height_inches = slide_dimensions
+ else:
+ # Fallback: estimate from image size at CONVERSION_DPI
+ slide_width_inches = orig_w / CONVERSION_DPI
+ slide_height_inches = orig_h / CONVERSION_DPI
+
+ x_scale = orig_w / slide_width_inches
+ y_scale = orig_h / slide_height_inches
+
+ # Create a highlight overlay
+ overlay = Image.new("RGBA", img.size, (255, 255, 255, 0))
+ overlay_draw = ImageDraw.Draw(overlay)
+
+ # Highlight each placeholder region
+ for region in regions:
+ # Convert from inches to pixels in the original image
+ px_left = int(region["left"] * x_scale)
+ px_top = int(region["top"] * y_scale)
+ px_width = int(region["width"] * x_scale)
+ px_height = int(region["height"] * y_scale)
+
+ # Draw highlight outline with red color and thick stroke
+ # Using a bright red outline instead of fill
+ stroke_width = max(
+ 5, min(orig_w, orig_h) // 150
+ ) # Thicker proportional stroke width
+ overlay_draw.rectangle(
+ [(px_left, px_top), (px_left + px_width, px_top + px_height)],
+ outline=(255, 0, 0, 255), # Bright red, fully opaque
+ width=stroke_width,
+ )
+
+ # Composite the overlay onto the image using alpha blending
+ img = Image.alpha_composite(img, overlay)
+ # Convert back to RGB for JPEG saving
+ img = img.convert("RGB")
+
+ img.thumbnail((width, height), Image.Resampling.LANCZOS)
+ w, h = img.size
+ tx = x + (width - w) // 2
+ ty = y_thumbnail + (height - h) // 2
+ grid.paste(img, (tx, ty))
+
+ # Add border
+ if BORDER_WIDTH > 0:
+ draw.rectangle(
+ [
+ (tx - BORDER_WIDTH, ty - BORDER_WIDTH),
+ (tx + w + BORDER_WIDTH - 1, ty + h + BORDER_WIDTH - 1),
+ ],
+ outline="gray",
+ width=BORDER_WIDTH,
+ )
+
+ return grid
+
+
+if __name__ == "__main__":
+ main()
diff --git a/scientific-skills/document-skills/xlsx/LICENSE.txt b/scientific-skills/document-skills/xlsx/LICENSE.txt
new file mode 100644
index 0000000..c55ab42
--- /dev/null
+++ b/scientific-skills/document-skills/xlsx/LICENSE.txt
@@ -0,0 +1,30 @@
+© 2025 Anthropic, PBC. All rights reserved.
+
+LICENSE: Use of these materials (including all code, prompts, assets, files,
+and other components of this Skill) is governed by your agreement with
+Anthropic regarding use of Anthropic's services. If no separate agreement
+exists, use is governed by Anthropic's Consumer Terms of Service or
+Commercial Terms of Service, as applicable:
+https://www.anthropic.com/legal/consumer-terms
+https://www.anthropic.com/legal/commercial-terms
+Your applicable agreement is referred to as the "Agreement." "Services" are
+as defined in the Agreement.
+
+ADDITIONAL RESTRICTIONS: Notwithstanding anything in the Agreement to the
+contrary, users may not:
+
+- Extract these materials from the Services or retain copies of these
+ materials outside the Services
+- Reproduce or copy these materials, except for temporary copies created
+ automatically during authorized use of the Services
+- Create derivative works based on these materials
+- Distribute, sublicense, or transfer these materials to any third party
+- Make, offer to sell, sell, or import any inventions embodied in these
+ materials
+- Reverse engineer, decompile, or disassemble these materials
+
+The receipt, viewing, or possession of these materials does not convey or
+imply any license or right beyond those expressly granted above.
+
+Anthropic retains all right, title, and interest in these materials,
+including all copyrights, patents, and other intellectual property rights.
diff --git a/scientific-skills/document-skills/xlsx/SKILL.md b/scientific-skills/document-skills/xlsx/SKILL.md
new file mode 100644
index 0000000..50029dc
--- /dev/null
+++ b/scientific-skills/document-skills/xlsx/SKILL.md
@@ -0,0 +1,323 @@
+---
+name: xlsx
+description: "Spreadsheet toolkit (.xlsx/.csv). Create/edit with formulas/formatting, analyze data, visualization, recalculate formulas, for spreadsheet processing and analysis."
+license: Proprietary. LICENSE.txt has complete terms
+---
+
+# Requirements for Outputs
+
+## All Excel files
+
+### Zero Formula Errors
+- Every Excel model MUST be delivered with ZERO formula errors (#REF!, #DIV/0!, #VALUE!, #N/A, #NAME?)
+
+### Preserve Existing Templates (when updating templates)
+- Study and EXACTLY match existing format, style, and conventions when modifying files
+- Never impose standardized formatting on files with established patterns
+- Existing template conventions ALWAYS override these guidelines
+
+## Financial models
+
+### Color Coding Standards
+Unless otherwise stated by the user or existing template
+
+#### Industry-Standard Color Conventions
+- **Blue text (RGB: 0,0,255)**: Hardcoded inputs, and numbers users will change for scenarios
+- **Black text (RGB: 0,0,0)**: ALL formulas and calculations
+- **Green text (RGB: 0,128,0)**: Links pulling from other worksheets within same workbook
+- **Red text (RGB: 255,0,0)**: External links to other files
+- **Yellow background (RGB: 255,255,0)**: Key assumptions needing attention or cells that need to be updated
+
+### Number Formatting Standards
+
+#### Required Format Rules
+- **Years**: Format as text strings (e.g., "2024" not "2,024")
+- **Currency**: Use $#,##0 format; ALWAYS specify units in headers ("Revenue ($mm)")
+- **Zeros**: Use number formatting to make all zeros "-", including percentages (e.g., "$#,##0;($#,##0);-")
+- **Percentages**: Default to 0.0% format (one decimal)
+- **Multiples**: Format as 0.0x for valuation multiples (EV/EBITDA, P/E)
+- **Negative numbers**: Use parentheses (123) not minus -123
+
+### Formula Construction Rules
+
+#### Assumptions Placement
+- Place ALL assumptions (growth rates, margins, multiples, etc.) in separate assumption cells
+- Use cell references instead of hardcoded values in formulas
+- Example: Use =B5*(1+$B$6) instead of =B5*1.05
+
+#### Formula Error Prevention
+- Verify all cell references are correct
+- Check for off-by-one errors in ranges
+- Ensure consistent formulas across all projection periods
+- Test with edge cases (zero values, negative numbers)
+- Verify no unintended circular references
+
+#### Documentation Requirements for Hardcodes
+- Comment or in cells beside (if end of table). Format: "Source: [System/Document], [Date], [Specific Reference], [URL if applicable]"
+- Examples:
+ - "Source: Company 10-K, FY2024, Page 45, Revenue Note, [SEC EDGAR URL]"
+ - "Source: Company 10-Q, Q2 2025, Exhibit 99.1, [SEC EDGAR URL]"
+ - "Source: Bloomberg Terminal, 8/15/2025, AAPL US Equity"
+ - "Source: FactSet, 8/20/2025, Consensus Estimates Screen"
+
+# XLSX creation, editing, and analysis
+
+## Overview
+
+Create, edit, or analyze Excel spreadsheets with formulas, formatting, and data analysis. Apply this skill for spreadsheet processing using openpyxl and pandas. Recalculate formulas and ensure zero errors for publication-quality outputs.
+
+## Visual Enhancement with Scientific Schematics
+
+**When creating documents with this skill, always consider adding scientific diagrams and schematics to enhance visual communication.**
+
+If your document does not already contain schematics or diagrams:
+- Use the **scientific-schematics** skill to generate AI-powered publication-quality diagrams
+- Simply describe your desired diagram in natural language
+- Nano Banana Pro will automatically generate, review, and refine the schematic
+
+**For new documents:** Scientific schematics should be generated by default to visually represent key concepts, workflows, architectures, or relationships described in the text.
+
+**How to generate schematics:**
+```bash
+python scripts/generate_schematic.py "your diagram description" -o figures/output.png
+```
+
+The AI will automatically:
+- Create publication-quality images with proper formatting
+- Review and refine through multiple iterations
+- Ensure accessibility (colorblind-friendly, high contrast)
+- Save outputs in the figures/ directory
+
+**When to add schematics:**
+- Spreadsheet workflow diagrams
+- Data processing pipeline illustrations
+- Formula calculation flow diagrams
+- Financial model structure diagrams
+- Data analysis flowcharts
+- Any complex concept that benefits from visualization
+
+For detailed guidance on creating schematics, refer to the scientific-schematics skill documentation.
+
+---
+
+## Important Requirements
+
+**LibreOffice Required for Formula Recalculation**: You can assume LibreOffice is installed for recalculating formula values using the `recalc.py` script. The script automatically configures LibreOffice on first run
+
+## Reading and analyzing data
+
+### Data analysis with pandas
+For data analysis, visualization, and basic operations, use **pandas** which provides powerful data manipulation capabilities:
+
+```python
+import pandas as pd
+
+# Read Excel
+df = pd.read_excel('file.xlsx') # Default: first sheet
+all_sheets = pd.read_excel('file.xlsx', sheet_name=None) # All sheets as dict
+
+# Analyze
+df.head() # Preview data
+df.info() # Column info
+df.describe() # Statistics
+
+# Write Excel
+df.to_excel('output.xlsx', index=False)
+```
+
+## Excel File Workflows
+
+## CRITICAL: Use Formulas, Not Hardcoded Values
+
+**Always use Excel formulas instead of calculating values in Python and hardcoding them.** This ensures the spreadsheet remains dynamic and updateable.
+
+### ❌ WRONG - Hardcoding Calculated Values
+```python
+# Bad: Calculating in Python and hardcoding result
+total = df['Sales'].sum()
+sheet['B10'] = total # Hardcodes 5000
+
+# Bad: Computing growth rate in Python
+growth = (df.iloc[-1]['Revenue'] - df.iloc[0]['Revenue']) / df.iloc[0]['Revenue']
+sheet['C5'] = growth # Hardcodes 0.15
+
+# Bad: Python calculation for average
+avg = sum(values) / len(values)
+sheet['D20'] = avg # Hardcodes 42.5
+```
+
+### ✅ CORRECT - Using Excel Formulas
+```python
+# Good: Let Excel calculate the sum
+sheet['B10'] = '=SUM(B2:B9)'
+
+# Good: Growth rate as Excel formula
+sheet['C5'] = '=(C4-C2)/C2'
+
+# Good: Average using Excel function
+sheet['D20'] = '=AVERAGE(D2:D19)'
+```
+
+This applies to ALL calculations - totals, percentages, ratios, differences, etc. The spreadsheet should be able to recalculate when source data changes.
+
+## Common Workflow
+1. **Choose tool**: pandas for data, openpyxl for formulas/formatting
+2. **Create/Load**: Create new workbook or load existing file
+3. **Modify**: Add/edit data, formulas, and formatting
+4. **Save**: Write to file
+5. **Recalculate formulas (MANDATORY IF USING FORMULAS)**: Use the recalc.py script
+ ```bash
+ python recalc.py output.xlsx
+ ```
+6. **Verify and fix any errors**:
+ - The script returns JSON with error details
+ - If `status` is `errors_found`, check `error_summary` for specific error types and locations
+ - Fix the identified errors and recalculate again
+ - Common errors to fix:
+ - `#REF!`: Invalid cell references
+ - `#DIV/0!`: Division by zero
+ - `#VALUE!`: Wrong data type in formula
+ - `#NAME?`: Unrecognized formula name
+
+### Creating new Excel files
+
+```python
+# Using openpyxl for formulas and formatting
+from openpyxl import Workbook
+from openpyxl.styles import Font, PatternFill, Alignment
+
+wb = Workbook()
+sheet = wb.active
+
+# Add data
+sheet['A1'] = 'Hello'
+sheet['B1'] = 'World'
+sheet.append(['Row', 'of', 'data'])
+
+# Add formula
+sheet['B2'] = '=SUM(A1:A10)'
+
+# Formatting
+sheet['A1'].font = Font(bold=True, color='FF0000')
+sheet['A1'].fill = PatternFill('solid', start_color='FFFF00')
+sheet['A1'].alignment = Alignment(horizontal='center')
+
+# Column width
+sheet.column_dimensions['A'].width = 20
+
+wb.save('output.xlsx')
+```
+
+### Editing existing Excel files
+
+```python
+# Using openpyxl to preserve formulas and formatting
+from openpyxl import load_workbook
+
+# Load existing file
+wb = load_workbook('existing.xlsx')
+sheet = wb.active # or wb['SheetName'] for specific sheet
+
+# Working with multiple sheets
+for sheet_name in wb.sheetnames:
+ sheet = wb[sheet_name]
+ print(f"Sheet: {sheet_name}")
+
+# Modify cells
+sheet['A1'] = 'New Value'
+sheet.insert_rows(2) # Insert row at position 2
+sheet.delete_cols(3) # Delete column 3
+
+# Add new sheet
+new_sheet = wb.create_sheet('NewSheet')
+new_sheet['A1'] = 'Data'
+
+wb.save('modified.xlsx')
+```
+
+## Recalculating formulas
+
+Excel files created or modified by openpyxl contain formulas as strings but not calculated values. Use the provided `recalc.py` script to recalculate formulas:
+
+```bash
+python recalc.py [timeout_seconds]
+```
+
+Example:
+```bash
+python recalc.py output.xlsx 30
+```
+
+The script:
+- Automatically sets up LibreOffice macro on first run
+- Recalculates all formulas in all sheets
+- Scans ALL cells for Excel errors (#REF!, #DIV/0!, etc.)
+- Returns JSON with detailed error locations and counts
+- Works on both Linux and macOS
+
+## Formula Verification Checklist
+
+Quick checks to ensure formulas work correctly:
+
+### Essential Verification
+- [ ] **Test 2-3 sample references**: Verify they pull correct values before building full model
+- [ ] **Column mapping**: Confirm Excel columns match (e.g., column 64 = BL, not BK)
+- [ ] **Row offset**: Remember Excel rows are 1-indexed (DataFrame row 5 = Excel row 6)
+
+### Common Pitfalls
+- [ ] **NaN handling**: Check for null values with `pd.notna()`
+- [ ] **Far-right columns**: FY data often in columns 50+
+- [ ] **Multiple matches**: Search all occurrences, not just first
+- [ ] **Division by zero**: Check denominators before using `/` in formulas (#DIV/0!)
+- [ ] **Wrong references**: Verify all cell references point to intended cells (#REF!)
+- [ ] **Cross-sheet references**: Use correct format (Sheet1!A1) for linking sheets
+
+### Formula Testing Strategy
+- [ ] **Start small**: Test formulas on 2-3 cells before applying broadly
+- [ ] **Verify dependencies**: Check all cells referenced in formulas exist
+- [ ] **Test edge cases**: Include zero, negative, and very large values
+
+### Interpreting recalc.py Output
+The script returns JSON with error details:
+```json
+{
+ "status": "success", // or "errors_found"
+ "total_errors": 0, // Total error count
+ "total_formulas": 42, // Number of formulas in file
+ "error_summary": { // Only present if errors found
+ "#REF!": {
+ "count": 2,
+ "locations": ["Sheet1!B5", "Sheet1!C10"]
+ }
+ }
+}
+```
+
+## Best Practices
+
+### Library Selection
+- **pandas**: Best for data analysis, bulk operations, and simple data export
+- **openpyxl**: Best for complex formatting, formulas, and Excel-specific features
+
+### Working with openpyxl
+- Cell indices are 1-based (row=1, column=1 refers to cell A1)
+- Use `data_only=True` to read calculated values: `load_workbook('file.xlsx', data_only=True)`
+- **Warning**: If opened with `data_only=True` and saved, formulas are replaced with values and permanently lost
+- For large files: Use `read_only=True` for reading or `write_only=True` for writing
+- Formulas are preserved but not evaluated - use recalc.py to update values
+
+### Working with pandas
+- Specify data types to avoid inference issues: `pd.read_excel('file.xlsx', dtype={'id': str})`
+- For large files, read specific columns: `pd.read_excel('file.xlsx', usecols=['A', 'C', 'E'])`
+- Handle dates properly: `pd.read_excel('file.xlsx', parse_dates=['date_column'])`
+
+## Code Style Guidelines
+**IMPORTANT**: When generating Python code for Excel operations:
+- Write minimal, concise Python code without unnecessary comments
+- Avoid verbose variable names and redundant operations
+- Avoid unnecessary print statements
+
+**For Excel files themselves**:
+- Add comments to cells with complex formulas or important assumptions
+- Document data sources for hardcoded values
+- Include notes for key calculations and model sections
\ No newline at end of file
diff --git a/scientific-skills/document-skills/xlsx/recalc.py b/scientific-skills/document-skills/xlsx/recalc.py
new file mode 100644
index 0000000..102e157
--- /dev/null
+++ b/scientific-skills/document-skills/xlsx/recalc.py
@@ -0,0 +1,178 @@
+#!/usr/bin/env python3
+"""
+Excel Formula Recalculation Script
+Recalculates all formulas in an Excel file using LibreOffice
+"""
+
+import json
+import sys
+import subprocess
+import os
+import platform
+from pathlib import Path
+from openpyxl import load_workbook
+
+
+def setup_libreoffice_macro():
+ """Setup LibreOffice macro for recalculation if not already configured"""
+ if platform.system() == 'Darwin':
+ macro_dir = os.path.expanduser('~/Library/Application Support/LibreOffice/4/user/basic/Standard')
+ else:
+ macro_dir = os.path.expanduser('~/.config/libreoffice/4/user/basic/Standard')
+
+ macro_file = os.path.join(macro_dir, 'Module1.xba')
+
+ if os.path.exists(macro_file):
+ with open(macro_file, 'r') as f:
+ if 'RecalculateAndSave' in f.read():
+ return True
+
+ if not os.path.exists(macro_dir):
+ subprocess.run(['soffice', '--headless', '--terminate_after_init'],
+ capture_output=True, timeout=10)
+ os.makedirs(macro_dir, exist_ok=True)
+
+ macro_content = '''
+
+
+ Sub RecalculateAndSave()
+ ThisComponent.calculateAll()
+ ThisComponent.store()
+ ThisComponent.close(True)
+ End Sub
+'''
+
+ try:
+ with open(macro_file, 'w') as f:
+ f.write(macro_content)
+ return True
+ except Exception:
+ return False
+
+
+def recalc(filename, timeout=30):
+ """
+ Recalculate formulas in Excel file and report any errors
+
+ Args:
+ filename: Path to Excel file
+ timeout: Maximum time to wait for recalculation (seconds)
+
+ Returns:
+ dict with error locations and counts
+ """
+ if not Path(filename).exists():
+ return {'error': f'File {filename} does not exist'}
+
+ abs_path = str(Path(filename).absolute())
+
+ if not setup_libreoffice_macro():
+ return {'error': 'Failed to setup LibreOffice macro'}
+
+ cmd = [
+ 'soffice', '--headless', '--norestore',
+ 'vnd.sun.star.script:Standard.Module1.RecalculateAndSave?language=Basic&location=application',
+ abs_path
+ ]
+
+ # Handle timeout command differences between Linux and macOS
+ if platform.system() != 'Windows':
+ timeout_cmd = 'timeout' if platform.system() == 'Linux' else None
+ if platform.system() == 'Darwin':
+ # Check if gtimeout is available on macOS
+ try:
+ subprocess.run(['gtimeout', '--version'], capture_output=True, timeout=1, check=False)
+ timeout_cmd = 'gtimeout'
+ except (FileNotFoundError, subprocess.TimeoutExpired):
+ pass
+
+ if timeout_cmd:
+ cmd = [timeout_cmd, str(timeout)] + cmd
+
+ result = subprocess.run(cmd, capture_output=True, text=True)
+
+ if result.returncode != 0 and result.returncode != 124: # 124 is timeout exit code
+ error_msg = result.stderr or 'Unknown error during recalculation'
+ if 'Module1' in error_msg or 'RecalculateAndSave' not in error_msg:
+ return {'error': 'LibreOffice macro not configured properly'}
+ else:
+ return {'error': error_msg}
+
+ # Check for Excel errors in the recalculated file - scan ALL cells
+ try:
+ wb = load_workbook(filename, data_only=True)
+
+ excel_errors = ['#VALUE!', '#DIV/0!', '#REF!', '#NAME?', '#NULL!', '#NUM!', '#N/A']
+ error_details = {err: [] for err in excel_errors}
+ total_errors = 0
+
+ for sheet_name in wb.sheetnames:
+ ws = wb[sheet_name]
+ # Check ALL rows and columns - no limits
+ for row in ws.iter_rows():
+ for cell in row:
+ if cell.value is not None and isinstance(cell.value, str):
+ for err in excel_errors:
+ if err in cell.value:
+ location = f"{sheet_name}!{cell.coordinate}"
+ error_details[err].append(location)
+ total_errors += 1
+ break
+
+ wb.close()
+
+ # Build result summary
+ result = {
+ 'status': 'success' if total_errors == 0 else 'errors_found',
+ 'total_errors': total_errors,
+ 'error_summary': {}
+ }
+
+ # Add non-empty error categories
+ for err_type, locations in error_details.items():
+ if locations:
+ result['error_summary'][err_type] = {
+ 'count': len(locations),
+ 'locations': locations[:20] # Show up to 20 locations
+ }
+
+ # Add formula count for context - also check ALL cells
+ wb_formulas = load_workbook(filename, data_only=False)
+ formula_count = 0
+ for sheet_name in wb_formulas.sheetnames:
+ ws = wb_formulas[sheet_name]
+ for row in ws.iter_rows():
+ for cell in row:
+ if cell.value and isinstance(cell.value, str) and cell.value.startswith('='):
+ formula_count += 1
+ wb_formulas.close()
+
+ result['total_formulas'] = formula_count
+
+ return result
+
+ except Exception as e:
+ return {'error': str(e)}
+
+
+def main():
+ if len(sys.argv) < 2:
+ print("Usage: python recalc.py [timeout_seconds]")
+ print("\nRecalculates all formulas in an Excel file using LibreOffice")
+ print("\nReturns JSON with error details:")
+ print(" - status: 'success' or 'errors_found'")
+ print(" - total_errors: Total number of Excel errors found")
+ print(" - total_formulas: Number of formulas in the file")
+ print(" - error_summary: Breakdown by error type with locations")
+ print(" - #VALUE!, #DIV/0!, #REF!, #NAME?, #NULL!, #NUM!, #N/A")
+ sys.exit(1)
+
+ filename = sys.argv[1]
+ timeout = int(sys.argv[2]) if len(sys.argv) > 2 else 30
+
+ result = recalc(filename, timeout)
+ print(json.dumps(result, indent=2))
+
+
+if __name__ == '__main__':
+ main()
\ No newline at end of file
diff --git a/scientific-skills/latex-posters/README.md b/scientific-skills/latex-posters/README.md
new file mode 100644
index 0000000..64ecc9d
--- /dev/null
+++ b/scientific-skills/latex-posters/README.md
@@ -0,0 +1,417 @@
+# LaTeX Research Poster Generation Skill
+
+Create professional, publication-ready research posters for conferences and academic presentations using LaTeX.
+
+## Overview
+
+This skill provides comprehensive guidance for creating research posters with three major LaTeX packages:
+- **beamerposter**: Traditional academic posters, familiar Beamer syntax
+- **tikzposter**: Modern, colorful designs with TikZ integration
+- **baposter**: Structured multi-column layouts with automatic positioning
+
+## Quick Start
+
+### 1. Choose a Template
+
+Browse templates in `assets/`:
+- `beamerposter_template.tex` - Classic academic style
+- `tikzposter_template.tex` - Modern, colorful design
+- `baposter_template.tex` - Structured multi-column layout
+
+### 2. Customize Content
+
+Edit the template with your research:
+- Title, authors, affiliations
+- Introduction, methods, results, conclusions
+- Replace placeholder figures with your images
+- Update references and acknowledgments
+
+### 3. Configure for Full Page
+
+Posters should span the entire page with minimal margins:
+
+```latex
+% beamerposter - full page setup
+\documentclass[final,t]{beamer}
+\usepackage[size=a0,scale=1.4,orientation=portrait]{beamerposter}
+\setbeamersize{text margin left=5mm, text margin right=5mm}
+\usepackage[margin=10mm]{geometry}
+
+% tikzposter - full page setup
+\documentclass[25pt,a0paper,portrait,margin=10mm,innermargin=15mm]{tikzposter}
+
+% baposter - full page setup
+\documentclass[a0paper,portrait,fontscale=0.285]{baposter}
+```
+
+### 4. Compile
+
+```bash
+pdflatex poster.tex
+
+# Or for better font support:
+lualatex poster.tex
+xelatex poster.tex
+```
+
+### 5. Review PDF Quality
+
+**Essential before printing!**
+
+```bash
+# Run automated checks
+./scripts/review_poster.sh poster.pdf
+
+# Manual verification (see checklist below)
+```
+
+## Key Features
+
+### Full Page Coverage
+
+All templates configured to maximize content area:
+- Minimal outer margins (5-15mm)
+- Optimal spacing between columns (15-20mm)
+- Proper block padding for readability
+- No wasted white space
+
+### PDF Quality Control
+
+**Automated Checks** (`review_poster.sh`):
+- Page size verification
+- Font embedding check
+- Image resolution analysis
+- File size optimization
+
+**Manual Verification** (`assets/poster_quality_checklist.md`):
+- Visual inspection at 100% zoom
+- Reduced-scale print test (25%)
+- Typography and spacing review
+- Content completeness check
+
+### Design Principles
+
+All templates follow evidence-based poster design:
+- **Typography**: 72pt+ title, 48-72pt headers, 24-36pt body text
+- **Color**: High contrast (≥4.5:1), color-blind friendly palettes
+- **Layout**: Clear visual hierarchy, logical flow
+- **Content**: 300-800 words maximum, 40-50% visual content
+
+## Common Poster Sizes
+
+Templates support all standard sizes:
+
+| Size | Dimensions | Configuration |
+|------|------------|---------------|
+| A0 | 841 × 1189 mm | `size=a0` or `a0paper` |
+| A1 | 594 × 841 mm | `size=a1` or `a1paper` |
+| 36×48" | 914 × 1219 mm | Custom page size |
+| 42×56" | 1067 × 1422 mm | Custom page size |
+
+## Documentation
+
+### Reference Guides
+
+**Comprehensive Documentation** (in `references/`):
+
+1. **`latex_poster_packages.md`** (746 lines)
+ - Detailed comparison of beamerposter, tikzposter, baposter
+ - Package-specific syntax and examples
+ - Strengths, limitations, best use cases
+ - Theme and color customization
+ - Compilation tips and troubleshooting
+
+2. **`poster_design_principles.md`** (807 lines)
+ - Visual hierarchy and white space
+ - Typography: font selection, sizing, readability
+ - Color theory: schemes, contrast, accessibility
+ - Color-blind friendly palettes
+ - Icons, graphics, and visual elements
+ - Common design mistakes to avoid
+
+3. **`poster_layout_design.md`** (650+ lines)
+ - Grid systems (2, 3, 4-column layouts)
+ - Visual flow and reading patterns
+ - Spatial organization strategies
+ - White space management
+ - Block and box design
+ - Layout patterns by research type
+
+4. **`poster_content_guide.md`** (900+ lines)
+ - Content strategy (3-5 minute rule)
+ - Word budgets by section
+ - Visual-to-text ratio (40-50% visual)
+ - Section-specific writing guidance
+ - Figure integration and captions
+ - From paper to poster adaptation
+
+### Tools and Assets
+
+**Scripts** (in `scripts/`):
+- `review_poster.sh`: Automated PDF quality check
+ - Page size verification
+ - Font embedding check
+ - Image resolution analysis
+ - File size assessment
+
+**Checklists** (in `assets/`):
+- `poster_quality_checklist.md`: Comprehensive pre-printing checklist
+ - Pre-compilation checks
+ - PDF quality verification
+ - Visual inspection items
+ - Accessibility checks
+ - Peer review guidelines
+ - Final printing checklist
+
+**Templates** (in `assets/`):
+- `beamerposter_template.tex`: Full working template
+- `tikzposter_template.tex`: Full working template
+- `baposter_template.tex`: Full working template
+
+## Workflow
+
+### Recommended Poster Creation Process
+
+**1. Planning** (before LaTeX)
+- Determine conference requirements (size, orientation)
+- Identify 3-5 key results to highlight
+- Create figures (300+ DPI)
+- Draft 300-800 word content outline
+
+**2. Template Selection**
+- Choose package based on needs:
+ - **beamerposter**: Traditional conferences, institutional branding
+ - **tikzposter**: Modern conferences, creative fields
+ - **baposter**: Multi-section posters, structured layouts
+
+**3. Content Integration**
+- Copy template and customize
+- Replace placeholder text
+- Add figures and ensure high resolution
+- Configure colors to match branding
+
+**4. Compilation & Review**
+- Compile to PDF
+- Run `review_poster.sh` for automated checks
+- Review visually at 100% zoom
+- Check against `poster_quality_checklist.md`
+
+**5. Test Print**
+- **Critical step!** Print at 25% scale
+- A0 → A4 paper, 36×48" → Letter paper
+- View from 2-3 feet (simulates 8-12 feet for full poster)
+- Verify readability and colors
+
+**6. Revisions**
+- Fix any issues identified
+- Proofread carefully (errors are magnified!)
+- Get colleague feedback
+- Final compilation
+
+**7. Printing**
+- Verify page size: `pdfinfo poster.pdf`
+- Check fonts embedded: `pdffonts poster.pdf`
+- Send to professional printer 2-3 days before deadline
+- Keep backup copy
+
+## Troubleshooting
+
+### Large White Margins
+
+**Problem**: Excessive white space around poster edges
+
+**Solution**:
+```latex
+% beamerposter
+\setbeamersize{text margin left=5mm, text margin right=5mm}
+\usepackage[margin=10mm]{geometry}
+
+% tikzposter
+\documentclass[..., margin=5mm, innermargin=10mm]{tikzposter}
+
+% baposter
+\documentclass[a0paper, margin=5mm]{baposter}
+```
+
+### Content Cut Off
+
+**Problem**: Text or figures extending beyond page
+
+**Solution**:
+- Check total width: columns + spacing + margins = pagewidth
+- Reduce column widths or spacing
+- Debug with visible page boundary:
+```latex
+\usepackage{eso-pic}
+\AddToShipoutPictureBG{
+ \AtPageLowerLeft{
+ \put(0,0){\framebox(\LenToUnit{\paperwidth},\LenToUnit{\paperheight}){}}
+ }
+}
+```
+
+### Blurry Images
+
+**Problem**: Pixelated or low-quality figures
+
+**Solution**:
+- Use vector graphics (PDF, SVG) when possible
+- Raster images: minimum 300 DPI at final print size
+- For A0 width (33.1"): 300 DPI = 9930 pixels minimum
+- Check with: `pdfimages -list poster.pdf`
+
+### Fonts Not Embedded
+
+**Problem**: Printer rejects PDF due to missing fonts
+
+**Solution**:
+```bash
+# Recompile with embedded fonts
+pdflatex -dEmbedAllFonts=true poster.tex
+
+# Verify embedding
+pdffonts poster.pdf
+# All fonts should show "yes" in "emb" column
+```
+
+### File Too Large
+
+**Problem**: PDF exceeds email size limit (>50MB)
+
+**Solution**:
+```bash
+# Compress for digital sharing
+gs -sDEVICE=pdfwrite -dCompatibilityLevel=1.4 \
+ -dPDFSETTINGS=/printer -dNOPAUSE -dQUIET -dBATCH \
+ -sOutputFile=poster_compressed.pdf poster.pdf
+
+# Keep original uncompressed version for printing
+```
+
+## Common Mistakes to Avoid
+
+### Content
+- ❌ Too much text (>1000 words)
+- ❌ Font sizes too small (<24pt body text)
+- ❌ No clear main message
+- ✅ 300-800 words, 30pt+ body text, 1-3 key findings
+
+### Design
+- ❌ Poor color contrast (<4.5:1)
+- ❌ Red-green color combinations (color-blind issue)
+- ❌ Cluttered layout with no white space
+- ✅ High contrast, accessible colors, generous spacing
+
+### Technical
+- ❌ Wrong poster dimensions
+- ❌ Low resolution images (<300 DPI)
+- ❌ Fonts not embedded
+- ✅ Verify specs, high-res images, embedded fonts
+
+## Package Comparison
+
+Quick reference for choosing the right package:
+
+| Feature | beamerposter | tikzposter | baposter |
+|---------|--------------|------------|----------|
+| **Learning Curve** | Easy (Beamer users) | Moderate | Moderate |
+| **Aesthetics** | Traditional | Modern | Professional |
+| **Customization** | Moderate | High (TikZ) | Structured |
+| **Compilation Speed** | Fast | Slower | Fast-Medium |
+| **Best For** | Academic conferences | Creative designs | Multi-column layouts |
+
+**Recommendation**:
+- First-time poster makers: **beamerposter** (familiar, simple)
+- Modern conferences: **tikzposter** (beautiful, flexible)
+- Complex layouts: **baposter** (automatic positioning)
+
+## Example Usage
+
+### In Scientific Writer CLI
+
+```
+> Create a research poster for NeurIPS conference on transformer attention
+
+The assistant will:
+1. Ask about poster size and orientation
+2. Generate complete LaTeX poster with your content
+3. Configure for full page coverage
+4. Provide compilation instructions
+5. Run quality checks on generated PDF
+```
+
+### Manual Creation
+
+```bash
+# 1. Copy template
+cp assets/tikzposter_template.tex my_poster.tex
+
+# 2. Edit content
+vim my_poster.tex
+
+# 3. Compile
+pdflatex my_poster.tex
+
+# 4. Review
+./scripts/review_poster.sh my_poster.pdf
+
+# 5. Test print at 25% scale
+# (A0 on A4 paper)
+
+# 6. Final printing
+```
+
+## Tips for Success
+
+### Content Strategy
+1. **One main message**: What's the one thing viewers should remember?
+2. **3-5 key figures**: Visual content dominates
+3. **300-800 words**: Less is more
+4. **Bullet points**: More scannable than paragraphs
+
+### Design Strategy
+1. **High contrast**: Dark on light or light on dark
+2. **Large fonts**: 30pt+ body text for readability from distance
+3. **White space**: 30-40% of poster should be empty
+4. **Visual hierarchy**: Vary sizes significantly (title 3× body text)
+
+### Technical Strategy
+1. **Test early**: Print at 25% scale before final printing
+2. **Vector graphics**: Use PDF/SVG when possible
+3. **Verify specs**: Check page size, fonts, resolution
+4. **Get feedback**: Ask colleague to review before printing
+
+## Additional Resources
+
+### Online Tools
+- **Color contrast checker**: https://webaim.org/resources/contrastchecker/
+- **Color blindness simulator**: https://www.color-blindness.com/coblis-color-blindness-simulator/
+- **Color palette generator**: https://coolors.co/
+
+### LaTeX Packages
+- `beamerposter`: Extends Beamer for poster-sized documents
+- `tikzposter`: Modern poster creation with TikZ
+- `baposter`: Box-based automatic poster layout
+- `qrcode`: Generate QR codes in LaTeX
+- `graphicx`: Include images
+- `tcolorbox`: Colored boxes and frames
+
+### Further Reading
+- All reference documents in `references/` directory
+- Quality checklist in `assets/poster_quality_checklist.md`
+- Package comparison in `references/latex_poster_packages.md`
+
+## Support
+
+For issues or questions:
+- Review reference documentation in `references/`
+- Check troubleshooting section above
+- Run automated review: `./scripts/review_poster.sh`
+- Use quality checklist: `assets/poster_quality_checklist.md`
+
+## Version
+
+LaTeX Poster Skill v1.0
+Compatible with: beamerposter, tikzposter, baposter
+Last updated: January 2025
+
diff --git a/scientific-skills/latex-posters/SKILL.md b/scientific-skills/latex-posters/SKILL.md
new file mode 100644
index 0000000..3ba3ef9
--- /dev/null
+++ b/scientific-skills/latex-posters/SKILL.md
@@ -0,0 +1,958 @@
+---
+name: latex-posters
+description: "Create professional research posters in LaTeX using beamerposter, tikzposter, or baposter. Support for conference presentations, academic posters, and scientific communication. Includes layout design, color schemes, multi-column formats, figure integration, and poster-specific best practices for visual communication."
+allowed-tools: [Read, Write, Edit, Bash]
+---
+
+# LaTeX Research Posters
+
+## Overview
+
+Research posters are a critical medium for scientific communication at conferences, symposia, and academic events. This skill provides comprehensive guidance for creating professional, visually appealing research posters using LaTeX packages. Generate publication-quality posters with proper layout, typography, color schemes, and visual hierarchy.
+
+## When to Use This Skill
+
+This skill should be used when:
+- Creating research posters for conferences, symposia, or poster sessions
+- Designing academic posters for university events or thesis defenses
+- Preparing visual summaries of research for public engagement
+- Converting scientific papers into poster format
+- Creating template posters for research groups or departments
+- Designing posters that comply with specific conference size requirements (A0, A1, 36×48", etc.)
+- Building posters with complex multi-column layouts
+- Integrating figures, tables, equations, and citations in poster format
+
+## Visual Enhancement with Scientific Schematics
+
+**⚠️ MANDATORY: Every research poster MUST include at least 2-3 AI-generated figures using the scientific-schematics skill.**
+
+This is not optional. Posters are primarily visual media - text-heavy posters fail to communicate effectively. Before finalizing any poster:
+1. Generate at minimum TWO schematics or diagrams
+2. Target 3-4 figures for comprehensive posters (methodology flowchart, key results visualization, conceptual framework)
+3. Figures should occupy 40-50% of poster area
+
+**How to generate figures:**
+- Use the **scientific-schematics** skill to generate AI-powered publication-quality diagrams
+- Simply describe your desired diagram in natural language
+- Nano Banana Pro will automatically generate, review, and refine the schematic
+
+**How to generate schematics:**
+```bash
+python scripts/generate_schematic.py "your diagram description" -o figures/output.png
+```
+
+The AI will automatically:
+- Create publication-quality images with proper formatting
+- Review and refine through multiple iterations
+- Ensure accessibility (colorblind-friendly, high contrast)
+- Save outputs in the figures/ directory
+
+**When to add schematics:**
+- Research methodology flowcharts for poster content
+- Conceptual framework diagrams
+- Experimental design visualizations
+- Data analysis pipeline diagrams
+- System architecture diagrams
+- Biological pathway illustrations
+- Any complex concept that benefits from visualization
+
+For detailed guidance on creating schematics, refer to the scientific-schematics skill documentation.
+
+---
+
+## Core Capabilities
+
+### 1. LaTeX Poster Packages
+
+Support for three major LaTeX poster packages, each with distinct advantages. For detailed comparison and package-specific guidance, refer to `references/latex_poster_packages.md`.
+
+**beamerposter**:
+- Extension of the Beamer presentation class
+- Familiar syntax for Beamer users
+- Excellent theme support and customization
+- Best for: Traditional academic posters, institutional branding
+
+**tikzposter**:
+- Modern, flexible design with TikZ integration
+- Built-in color themes and layout templates
+- Extensive customization through TikZ commands
+- Best for: Colorful, modern designs, custom graphics
+
+**baposter**:
+- Box-based layout system
+- Automatic spacing and positioning
+- Professional-looking default styles
+- Best for: Multi-column layouts, consistent spacing
+
+### 2. Poster Layout and Structure
+
+Create effective poster layouts following visual communication principles. For comprehensive layout guidance, refer to `references/poster_layout_design.md`.
+
+**Common Poster Sections**:
+- **Header/Title**: Title, authors, affiliations, logos
+- **Introduction/Background**: Research context and motivation
+- **Methods/Approach**: Methodology and experimental design
+- **Results**: Key findings with figures and data visualizations
+- **Conclusions**: Main takeaways and implications
+- **References**: Key citations (typically abbreviated)
+- **Acknowledgments**: Funding, collaborators, institutions
+
+**Layout Strategies**:
+- **Column-based layouts**: 2-column, 3-column, or 4-column grids
+- **Block-based layouts**: Flexible arrangement of content blocks
+- **Z-pattern flow**: Guide readers through content logically
+- **Visual hierarchy**: Use size, color, and spacing to emphasize key points
+
+### 3. Design Principles for Research Posters
+
+Apply evidence-based design principles for maximum impact. For detailed design guidance, refer to `references/poster_design_principles.md`.
+
+**Typography**:
+- Title: 72-120pt for visibility from distance
+- Section headers: 48-72pt
+- Body text: 24-36pt minimum for readability from 4-6 feet
+- Use sans-serif fonts (Arial, Helvetica, Calibri) for clarity
+- Limit to 2-3 font families maximum
+
+**Color and Contrast**:
+- Use high-contrast color schemes for readability
+- Institutional color palettes for branding
+- Color-blind friendly palettes (avoid red-green combinations)
+- White space is active space—don't overcrowd
+
+**Visual Elements**:
+- High-resolution figures (300 DPI minimum for print)
+- Large, clear labels on all figures
+- Consistent figure styling throughout
+- Strategic use of icons and graphics
+- Balance text with visual content (40-50% visual recommended)
+
+**Content Guidelines**:
+- **Less is more**: 300-800 words total recommended
+- Bullet points over paragraphs for scannability
+- Clear, concise messaging
+- Self-explanatory figures with minimal text explanation
+- QR codes for supplementary materials or online resources
+
+### 4. Standard Poster Sizes
+
+Support for international and conference-specific poster dimensions:
+
+**International Standards**:
+- A0 (841 × 1189 mm / 33.1 × 46.8 inches) - Most common European standard
+- A1 (594 × 841 mm / 23.4 × 33.1 inches) - Smaller format
+- A2 (420 × 594 mm / 16.5 × 23.4 inches) - Compact posters
+
+**North American Standards**:
+- 36 × 48 inches (914 × 1219 mm) - Common US conference size
+- 42 × 56 inches (1067 × 1422 mm) - Large format
+- 48 × 72 inches (1219 × 1829 mm) - Extra large
+
+**Orientation**:
+- Portrait (vertical) - Most common, traditional
+- Landscape (horizontal) - Better for wide content, timelines
+
+### 5. Package-Specific Templates
+
+Provide ready-to-use templates for each major package. Templates available in `assets/` directory.
+
+**beamerposter Templates**:
+- `beamerposter_classic.tex` - Traditional academic style
+- `beamerposter_modern.tex` - Clean, minimal design
+- `beamerposter_colorful.tex` - Vibrant theme with blocks
+
+**tikzposter Templates**:
+- `tikzposter_default.tex` - Standard tikzposter layout
+- `tikzposter_rays.tex` - Modern design with ray theme
+- `tikzposter_wave.tex` - Professional wave-style theme
+
+**baposter Templates**:
+- `baposter_portrait.tex` - Classic portrait layout
+- `baposter_landscape.tex` - Landscape multi-column
+- `baposter_minimal.tex` - Minimalist design
+
+### 6. Figure and Image Integration
+
+Optimize visual content for poster presentations:
+
+**Best Practices**:
+- Use vector graphics (PDF, SVG) when possible for scalability
+- Raster images: minimum 300 DPI at final print size
+- Consistent image styling (borders, captions, sizes)
+- Group related figures together
+- Use subfigures for comparisons
+
+**LaTeX Figure Commands**:
+```latex
+% Include graphics package
+\usepackage{graphicx}
+
+% Simple figure
+\includegraphics[width=0.8\linewidth]{figure.pdf}
+
+% Figure with caption in tikzposter
+\block{Results}{
+ \begin{tikzfigure}
+ \includegraphics[width=0.9\linewidth]{results.png}
+ \end{tikzfigure}
+}
+
+% Multiple subfigures
+\usepackage{subcaption}
+\begin{figure}
+ \begin{subfigure}{0.48\linewidth}
+ \includegraphics[width=\linewidth]{fig1.pdf}
+ \caption{Condition A}
+ \end{subfigure}
+ \begin{subfigure}{0.48\linewidth}
+ \includegraphics[width=\linewidth]{fig2.pdf}
+ \caption{Condition B}
+ \end{subfigure}
+\end{figure}
+```
+
+### 7. Color Schemes and Themes
+
+Provide professional color palettes for various contexts:
+
+**Academic Institution Colors**:
+- Match university or department branding
+- Use official color codes (RGB, CMYK, or LaTeX color definitions)
+
+**Scientific Color Palettes** (color-blind friendly):
+- Viridis: Professional gradient from purple to yellow
+- ColorBrewer: Research-tested palettes for data visualization
+- IBM Color Blind Safe: Accessible corporate palette
+
+**Package-Specific Theme Selection**:
+
+**beamerposter**:
+```latex
+\usetheme{Berlin}
+\usecolortheme{beaver}
+```
+
+**tikzposter**:
+```latex
+\usetheme{Rays}
+\usecolorstyle{Denmark}
+```
+
+**baposter**:
+```latex
+\begin{poster}{
+ background=plain,
+ bgColorOne=white,
+ headerColorOne=blue!70,
+ textborder=rounded
+}
+```
+
+### 8. Typography and Text Formatting
+
+Ensure readability and visual appeal:
+
+**Font Selection**:
+```latex
+% Sans-serif fonts recommended for posters
+\usepackage{helvet} % Helvetica
+\usepackage{avant} % Avant Garde
+\usepackage{sfmath} % Sans-serif math fonts
+
+% Set default to sans-serif
+\renewcommand{\familydefault}{\sfdefault}
+```
+
+**Text Sizing**:
+```latex
+% Adjust text sizes for visibility
+\setbeamerfont{title}{size=\VeryHuge}
+\setbeamerfont{author}{size=\Large}
+\setbeamerfont{institute}{size=\normalsize}
+```
+
+**Emphasis and Highlighting**:
+- Use bold for key terms: `\textbf{important}`
+- Color highlights sparingly: `\textcolor{blue}{highlight}`
+- Boxes for critical information
+- Avoid italics (harder to read from distance)
+
+### 9. QR Codes and Interactive Elements
+
+Enhance poster interactivity for modern conferences:
+
+**QR Code Integration**:
+```latex
+\usepackage{qrcode}
+
+% Link to paper, code repository, or supplementary materials
+\qrcode[height=2cm]{https://github.com/username/project}
+
+% QR code with caption
+\begin{center}
+ \qrcode[height=3cm]{https://doi.org/10.1234/paper}\\
+ \small Scan for full paper
+\end{center}
+```
+
+**Digital Enhancements**:
+- Link to GitHub repositories for code
+- Link to video presentations or demos
+- Link to interactive web visualizations
+- Link to supplementary data or appendices
+
+### 10. Compilation and Output
+
+Generate high-quality PDF output for printing or digital display:
+
+**Compilation Commands**:
+```bash
+# Basic compilation
+pdflatex poster.tex
+
+# With bibliography
+pdflatex poster.tex
+bibtex poster
+pdflatex poster.tex
+pdflatex poster.tex
+
+# For beamer-based posters
+lualatex poster.tex # Better font support
+xelatex poster.tex # Unicode and modern fonts
+```
+
+**Ensuring Full Page Coverage**:
+
+Posters should use the entire page without excessive margins. Configure packages correctly:
+
+**beamerposter - Full Page Setup**:
+```latex
+\documentclass[final,t]{beamer}
+\usepackage[size=a0,scale=1.4,orientation=portrait]{beamerposter}
+
+% Remove default beamer margins
+\setbeamersize{text margin left=0mm, text margin right=0mm}
+
+% Use geometry for precise control
+\usepackage[margin=10mm]{geometry} % 10mm margins all around
+
+% Remove navigation symbols
+\setbeamertemplate{navigation symbols}{}
+
+% Remove footline and headline if not needed
+\setbeamertemplate{footline}{}
+\setbeamertemplate{headline}{}
+```
+
+**tikzposter - Full Page Setup**:
+```latex
+\documentclass[
+ 25pt, % Font scaling
+ a0paper, % Paper size
+ portrait, % Orientation
+ margin=10mm, % Outer margins (minimal)
+ innermargin=15mm, % Space inside blocks
+ blockverticalspace=15mm, % Space between blocks
+ colspace=15mm, % Space between columns
+ subcolspace=8mm % Space between subcolumns
+]{tikzposter}
+
+% This ensures content fills the page
+```
+
+**baposter - Full Page Setup**:
+```latex
+\documentclass[a0paper,portrait,fontscale=0.285]{baposter}
+
+\begin{poster}{
+ grid=false,
+ columns=3,
+ colspacing=1.5em, % Space between columns
+ eyecatcher=true,
+ background=plain,
+ bgColorOne=white,
+ borderColor=blue!50,
+ headerheight=0.12\textheight, % 12% for header
+ textborder=roundedleft,
+ headerborder=closed,
+ boxheaderheight=2em % Consistent box header heights
+}
+% Content here
+\end{poster}
+```
+
+**Common Issues and Fixes**:
+
+**Problem**: Large white margins around poster
+```latex
+% Fix for beamerposter
+\setbeamersize{text margin left=5mm, text margin right=5mm}
+
+% Fix for tikzposter
+\documentclass[..., margin=5mm, innermargin=10mm]{tikzposter}
+
+% Fix for baposter - adjust in document class
+\documentclass[a0paper, margin=5mm]{baposter}
+```
+
+**Problem**: Content doesn't fill vertical space
+```latex
+% Use \vfill between sections to distribute space
+\block{Introduction}{...}
+\vfill
+\block{Methods}{...}
+\vfill
+\block{Results}{...}
+
+% Or manually adjust block spacing
+\vspace{1cm} % Add space between specific blocks
+```
+
+**Problem**: Poster extends beyond page boundaries
+```latex
+% Check total width calculation
+% For 3 columns with spacing:
+% Total = 3×columnwidth + 2×colspace + 2×margins
+% Ensure this equals \paperwidth
+
+% Debug by adding visible page boundary
+\usepackage{eso-pic}
+\AddToShipoutPictureBG{
+ \AtPageLowerLeft{
+ \put(0,0){\framebox(\LenToUnit{\paperwidth},\LenToUnit{\paperheight}){}}
+ }
+}
+```
+
+**Print Preparation**:
+- Generate PDF/X-1a for professional printing
+- Embed all fonts
+- Convert colors to CMYK if required
+- Check resolution of all images (minimum 300 DPI)
+- Add bleed area if required by printer (usually 3-5mm)
+- Verify page size matches requirements exactly
+
+**Digital Display**:
+- RGB color space for screen display
+- Optimize file size for email/web
+- Test readability on different screens
+
+### 11. PDF Review and Quality Control
+
+**CRITICAL**: Always review the generated PDF before printing or presenting. Use this systematic checklist:
+
+**Step 1: Page Size Verification**
+```bash
+# Check PDF dimensions (should match poster size exactly)
+pdfinfo poster.pdf | grep "Page size"
+
+# Expected outputs:
+# A0: 2384 x 3370 points (841 x 1189 mm)
+# 36x48": 2592 x 3456 points
+# A1: 1684 x 2384 points (594 x 841 mm)
+```
+
+**Step 2: Visual Inspection Checklist**
+
+Open PDF at 100% zoom and check:
+
+**Layout and Spacing**:
+- [ ] Content fills entire page (no large white margins)
+- [ ] Consistent spacing between columns
+- [ ] Consistent spacing between blocks/sections
+- [ ] All elements aligned properly (use ruler tool)
+- [ ] No overlapping text or figures
+- [ ] White space evenly distributed
+
+**Typography**:
+- [ ] Title clearly visible and large (72pt+)
+- [ ] Section headers readable (48-72pt)
+- [ ] Body text readable at 100% zoom (24-36pt minimum)
+- [ ] No text cutoff or running off edges
+- [ ] Consistent font usage throughout
+- [ ] All special characters render correctly (symbols, Greek letters)
+
+**Visual Elements**:
+- [ ] All figures display correctly
+- [ ] No pixelated or blurry images
+- [ ] Figure captions present and readable
+- [ ] Colors render as expected (not washed out or too dark)
+- [ ] Logos display clearly
+- [ ] QR codes visible and scannable
+
+**Content Completeness**:
+- [ ] Title and authors complete
+- [ ] All sections present (Intro, Methods, Results, Conclusions)
+- [ ] References included
+- [ ] Contact information visible
+- [ ] Acknowledgments (if applicable)
+- [ ] No placeholder text remaining (Lorem ipsum, TODO, etc.)
+
+**Technical Quality**:
+- [ ] No LaTeX compilation warnings in important areas
+- [ ] All citations resolved (no [?] marks)
+- [ ] All cross-references working
+- [ ] Page boundaries correct (no content cut off)
+
+**Step 3: Reduced-Scale Print Test**
+
+**Essential Pre-Printing Test**:
+```bash
+# Create reduced-size test print (25% of final size)
+# This simulates viewing full poster from ~8-10 feet
+
+# For A0 poster, print on A4 paper (24.7% scale)
+# For 36x48" poster, print on letter paper (~25% scale)
+```
+
+**Print Test Checklist**:
+- [ ] Title readable from 6 feet away
+- [ ] Section headers readable from 4 feet away
+- [ ] Body text readable from 2 feet away
+- [ ] Figures clear and understandable
+- [ ] Colors printed accurately
+- [ ] No obvious design flaws
+
+**Step 4: Digital Quality Checks**
+
+**Font Embedding Verification**:
+```bash
+# Check that all fonts are embedded (required for printing)
+pdffonts poster.pdf
+
+# All fonts should show "yes" in "emb" column
+# If any show "no", recompile with:
+pdflatex -dEmbedAllFonts=true poster.tex
+```
+
+**Image Resolution Check**:
+```bash
+# Extract image information
+pdfimages -list poster.pdf
+
+# Check that all images are at least 300 DPI
+# Formula: DPI = pixels / (inches in poster)
+# For A0 width (33.1"): 300 DPI = 9930 pixels minimum
+```
+
+**File Size Optimization**:
+```bash
+# For email/web, compress if needed (>50MB)
+gs -sDEVICE=pdfwrite -dCompatibilityLevel=1.4 \
+ -dPDFSETTINGS=/printer -dNOPAUSE -dQUIET -dBATCH \
+ -sOutputFile=poster_compressed.pdf poster.pdf
+
+# For printing, keep original (no compression)
+```
+
+**Step 5: Accessibility Check**
+
+**Color Contrast Verification**:
+- [ ] Text-background contrast ratio ≥ 4.5:1 (WCAG AA)
+- [ ] Important elements contrast ratio ≥ 7:1 (WCAG AAA)
+- Test online: https://webaim.org/resources/contrastchecker/
+
+**Color Blindness Simulation**:
+- [ ] View PDF through color blindness simulator
+- [ ] Information not lost with red-green simulation
+- [ ] Use Coblis (color-blindness.com) or similar tool
+
+**Step 6: Content Proofreading**
+
+**Systematic Review**:
+- [ ] Spell-check all text
+- [ ] Verify all author names and affiliations
+- [ ] Check all numbers and statistics for accuracy
+- [ ] Confirm all citations are correct
+- [ ] Review figure labels and captions
+- [ ] Check for typos in headers and titles
+
+**Peer Review**:
+- [ ] Ask colleague to review poster
+- [ ] 30-second test: Can they identify main message?
+- [ ] 5-minute review: Do they understand conclusions?
+- [ ] Note any confusing elements
+
+**Step 7: Technical Validation**
+
+**LaTeX Compilation Log Review**:
+```bash
+# Check for warnings in .log file
+grep -i "warning\|error\|overfull\|underfull" poster.log
+
+# Common issues to fix:
+# - Overfull hbox: Text extending beyond margins
+# - Underfull hbox: Excessive spacing
+# - Missing references: Citations not resolved
+# - Missing figures: Image files not found
+```
+
+**Fix Common Warnings**:
+```latex
+% Overfull hbox (text too wide)
+\usepackage{microtype} % Better spacing
+\sloppy % Allow slightly looser spacing
+\hyphenation{long-word} % Manual hyphenation
+
+% Missing fonts
+\usepackage[T1]{fontenc} % Better font encoding
+
+% Image not found
+% Ensure paths are correct and files exist
+\graphicspath{{./figures/}{./images/}}
+```
+
+**Step 8: Final Pre-Print Checklist**
+
+**Before Sending to Printer**:
+- [ ] PDF size exactly matches requirements (check with pdfinfo)
+- [ ] All fonts embedded (check with pdffonts)
+- [ ] Color mode correct (RGB for screen, CMYK for print if required)
+- [ ] Bleed area added if required (usually 3-5mm)
+- [ ] Crop marks visible if required
+- [ ] Test print completed and reviewed
+- [ ] File naming clear: [LastName]_[Conference]_Poster.pdf
+- [ ] Backup copy saved
+
+**Printing Specifications to Confirm**:
+- [ ] Paper type (matte vs. glossy)
+- [ ] Printing method (inkjet, large format, fabric)
+- [ ] Color profile (provided to printer if required)
+- [ ] Delivery deadline and shipping address
+- [ ] Tube or flat packaging preference
+
+**Digital Presentation Checklist**:
+- [ ] PDF size optimized (<10MB for email)
+- [ ] Tested on multiple PDF viewers (Adobe, Preview, etc.)
+- [ ] Displays correctly on different screens
+- [ ] QR codes tested and functional
+- [ ] Alternative formats prepared (PNG for social media)
+
+**Review Script** (Available in `scripts/review_poster.sh`):
+```bash
+#!/bin/bash
+# Automated poster PDF review script
+
+echo "Poster PDF Quality Check"
+echo "======================="
+
+# Check file exists
+if [ ! -f "$1" ]; then
+ echo "Error: File not found"
+ exit 1
+fi
+
+echo "File: $1"
+echo ""
+
+# Check page size
+echo "1. Page Dimensions:"
+pdfinfo "$1" | grep "Page size"
+echo ""
+
+# Check fonts
+echo "2. Font Embedding:"
+pdffonts "$1" | head -20
+echo ""
+
+# Check file size
+echo "3. File Size:"
+ls -lh "$1" | awk '{print $5}'
+echo ""
+
+# Count pages (should be 1 for poster)
+echo "4. Page Count:"
+pdfinfo "$1" | grep "Pages"
+echo ""
+
+echo "Manual checks required:"
+echo "- Visual inspection at 100% zoom"
+echo "- Reduced-scale print test (25%)"
+echo "- Color contrast verification"
+echo "- Proofreading for typos"
+```
+
+**Common PDF Issues and Solutions**:
+
+| Issue | Cause | Solution |
+|-------|-------|----------|
+| Large white margins | Incorrect margin settings | Reduce margin in documentclass |
+| Content cut off | Exceeds page boundaries | Check total width/height calculations |
+| Blurry images | Low resolution (<300 DPI) | Replace with higher resolution images |
+| Missing fonts | Fonts not embedded | Compile with -dEmbedAllFonts=true |
+| Wrong page size | Incorrect paper size setting | Verify documentclass paper size |
+| Colors look wrong | RGB vs CMYK mismatch | Convert color space for print |
+| File too large (>50MB) | Uncompressed images | Optimize images or compress PDF |
+| QR codes don't work | Too small or low resolution | Minimum 2×2cm, high contrast |
+
+### 11. Common Poster Content Patterns
+
+Effective content organization for different research types:
+
+**Experimental Research Poster**:
+1. Title and authors
+2. Introduction: Problem and hypothesis
+3. Methods: Experimental design (with diagram)
+4. Results: Key findings (2-4 main figures)
+5. Conclusions: Main takeaways (3-5 bullet points)
+6. Future work (optional)
+7. References and acknowledgments
+
+**Computational/Modeling Poster**:
+1. Title and authors
+2. Motivation: Problem statement
+3. Approach: Algorithm or model (with flowchart)
+4. Implementation: Technical details
+5. Results: Performance metrics and comparisons
+6. Applications: Use cases
+7. Code availability (QR code to GitHub)
+8. References
+
+**Review/Survey Poster**:
+1. Title and authors
+2. Scope: Topic overview
+3. Methods: Literature search strategy
+4. Key findings: Main themes (organized by category)
+5. Trends: Visualizations of publication patterns
+6. Gaps: Identified research needs
+7. Conclusions: Summary and implications
+8. References
+
+### 12. Accessibility and Inclusive Design
+
+Design posters that are accessible to diverse audiences:
+
+**Color Blindness Considerations**:
+- Avoid red-green combinations (most common color blindness)
+- Use patterns or shapes in addition to color
+- Test with color-blindness simulators
+- Provide high contrast (WCAG AA standard: 4.5:1 minimum)
+
+**Visual Impairment Accommodations**:
+- Large, clear fonts (minimum 24pt body text)
+- High contrast text and background
+- Clear visual hierarchy
+- Avoid complex textures or patterns in backgrounds
+
+**Language and Content**:
+- Clear, concise language
+- Define acronyms and jargon
+- International audience considerations
+- Consider multilingual QR code options for global conferences
+
+### 13. Poster Presentation Best Practices
+
+Guidance beyond LaTeX for effective poster sessions:
+
+**Content Strategy**:
+- Tell a story, don't just list facts
+- Focus on 1-3 main messages
+- Use visual abstract or graphical summary
+- Leave room for conversation (don't over-explain)
+
+**Physical Presentation Tips**:
+- Bring printed handouts or business cards with QR code
+- Prepare 30-second, 2-minute, and 5-minute verbal summaries
+- Stand to the side, not blocking the poster
+- Engage viewers with open-ended questions
+
+**Digital Backups**:
+- Save poster as PDF on mobile device
+- Prepare digital version for email sharing
+- Create social media-friendly image version
+- Have backup printed copy or digital display option
+
+## Workflow for Poster Creation
+
+### Stage 1: Planning and Content Development
+
+1. **Determine poster requirements**:
+ - Conference size specifications (A0, 36×48", etc.)
+ - Orientation (portrait vs. landscape)
+ - Submission deadlines and format requirements
+
+2. **Develop content outline**:
+ - Identify 1-3 core messages
+ - Select key figures (typically 3-6 main visuals)
+ - Draft concise text for each section (bullet points preferred)
+ - Aim for 300-800 words total
+
+3. **Choose LaTeX package**:
+ - beamerposter: If familiar with Beamer, need institutional themes
+ - tikzposter: For modern, colorful designs with flexibility
+ - baposter: For structured, professional multi-column layouts
+
+### Stage 2: Design and Layout
+
+1. **Select or create template**:
+ - Start with provided templates in `assets/`
+ - Customize color scheme to match branding
+ - Configure page size and orientation
+
+2. **Design layout structure**:
+ - Plan column structure (2, 3, or 4 columns)
+ - Map content flow (typically left-to-right, top-to-bottom)
+ - Allocate space for title (10-15%), content (70-80%), footer (5-10%)
+
+3. **Set typography**:
+ - Configure font sizes for different hierarchy levels
+ - Ensure minimum 24pt body text
+ - Test readability from 4-6 feet distance
+
+### Stage 3: Content Integration
+
+1. **Create poster header**:
+ - Title (concise, descriptive, 10-15 words)
+ - Authors and affiliations
+ - Institution logos (high-resolution)
+ - Conference logo if required
+
+2. **Populate content sections**:
+ - Keep text minimal and scannable
+ - Use bullet points, not paragraphs
+ - Write in active voice
+ - Integrate figures with clear captions
+
+3. **Add visual elements**:
+ - High-resolution figures (300 DPI minimum)
+ - Consistent styling across all figures
+ - Color-coded elements for emphasis
+ - QR codes for supplementary materials
+
+4. **Include references**:
+ - Cite key papers only (5-10 references typical)
+ - Use abbreviated citation style
+ - Consider QR code to full bibliography
+
+### Stage 4: Refinement and Testing
+
+1. **Review and iterate**:
+ - Check for typos and errors
+ - Verify all figures are high resolution
+ - Ensure consistent formatting
+ - Confirm color scheme works well together
+
+2. **Test readability**:
+ - Print at 25% scale and read from 2-3 feet (simulates poster from 8-12 feet)
+ - Check color on different monitors
+ - Verify QR codes function correctly
+ - Ask colleague to review
+
+3. **Optimize for printing**:
+ - Embed all fonts in PDF
+ - Verify image resolution
+ - Check PDF size requirements
+ - Include bleed area if required
+
+### Stage 5: Compilation and Delivery
+
+1. **Compile final PDF**:
+ ```bash
+ pdflatex poster.tex
+ # Or for better font support:
+ lualatex poster.tex
+ ```
+
+2. **Verify output quality**:
+ - Check all elements are visible and correctly positioned
+ - Zoom to 100% and inspect figure quality
+ - Verify colors match expectations
+ - Confirm PDF opens correctly on different viewers
+
+3. **Prepare for printing**:
+ - Export as PDF/X-1a if required
+ - Save backup copies
+ - Get test print on regular paper first
+ - Order professional printing 2-3 days before deadline
+
+4. **Create supplementary materials**:
+ - Save PNG/JPG version for social media
+ - Create handout version (8.5×11" summary)
+ - Prepare digital version for email sharing
+
+## Integration with Other Skills
+
+This skill works effectively with:
+- **Scientific Writing**: For developing poster content from papers
+- **Figure Creation**: For generating high-quality visualizations
+- **Literature Review**: For contextualizing research
+- **Data Analysis**: For creating result figures and charts
+
+## Common Pitfalls to Avoid
+
+**Design Mistakes**:
+- ❌ Too much text (over 1000 words)
+- ❌ Font sizes too small (under 24pt body text)
+- ❌ Low-contrast color combinations
+- ❌ Cluttered layout with no white space
+- ❌ Inconsistent styling across sections
+- ❌ Poor quality or pixelated images
+
+**Content Mistakes**:
+- ❌ No clear narrative or message
+- ❌ Too many research questions or objectives
+- ❌ Overuse of jargon without definitions
+- ❌ Results without context or interpretation
+- ❌ Missing author contact information
+
+**Technical Mistakes**:
+- ❌ Wrong poster dimensions for conference requirements
+- ❌ RGB colors sent to CMYK printer (color shift)
+- ❌ Fonts not embedded in PDF
+- ❌ File size too large for submission portal
+- ❌ QR codes too small or not tested
+
+**Best Practices**:
+- ✅ Follow conference size specifications exactly
+- ✅ Test print at reduced scale before final printing
+- ✅ Use high-contrast, accessible color schemes
+- ✅ Keep text minimal and highly scannable
+- ✅ Include clear contact information and QR codes
+- ✅ Balance text and visuals (40-50% visual content)
+- ✅ Proofread carefully (errors are magnified on posters!)
+
+## Package Installation
+
+Ensure required LaTeX packages are installed:
+
+```bash
+# For TeX Live (Linux/Mac)
+tlmgr install beamerposter tikzposter baposter
+
+# For MiKTeX (Windows)
+# Packages typically auto-install on first use
+
+# Additional recommended packages
+tlmgr install qrcode graphics xcolor tcolorbox subcaption
+```
+
+## Scripts and Automation
+
+Helper scripts available in `scripts/` directory:
+
+- `compile_poster.sh`: Automated compilation with error handling
+- `generate_template.py`: Interactive template generator
+- `resize_images.py`: Batch image optimization for posters
+- `poster_checklist.py`: Pre-submission validation tool
+
+## References
+
+Comprehensive reference files for detailed guidance:
+
+- `references/latex_poster_packages.md`: Detailed comparison of beamerposter, tikzposter, and baposter with examples
+- `references/poster_layout_design.md`: Layout principles, grid systems, and visual flow
+- `references/poster_design_principles.md`: Typography, color theory, visual hierarchy, and accessibility
+- `references/poster_content_guide.md`: Content organization, writing style, and section-specific guidance
+
+## Templates
+
+Ready-to-use poster templates in `assets/` directory:
+
+- beamerposter templates (classic, modern, colorful)
+- tikzposter templates (default, rays, wave, envelope)
+- baposter templates (portrait, landscape, minimal)
+- Example posters from various scientific disciplines
+- Color scheme definitions and institutional templates
+
+Load these templates and customize for your specific research and conference requirements.
+
diff --git a/scientific-skills/latex-posters/assets/baposter_template.tex b/scientific-skills/latex-posters/assets/baposter_template.tex
new file mode 100644
index 0000000..7c57eac
--- /dev/null
+++ b/scientific-skills/latex-posters/assets/baposter_template.tex
@@ -0,0 +1,257 @@
+% ==============================================================================
+% Research Poster Template - baposter
+% ==============================================================================
+% A structured, professional poster template using baposter
+% Excellent for multi-column layouts with automatic positioning
+% ==============================================================================
+
+\documentclass[a0paper,portrait,fontscale=0.285]{baposter}
+
+% Packages
+\usepackage{graphicx}
+\usepackage{amsmath,amssymb}
+\usepackage{booktabs}
+\usepackage{multicol}
+\usepackage{qrcode}
+\usepackage{hyperref}
+\usepackage{enumitem}
+
+% Set list spacing
+\setlist{nosep}
+
+% ==============================================================================
+% POSTER CONTENT - CUSTOMIZE BELOW
+% ==============================================================================
+
+\begin{document}
+
+\begin{poster}{
+ % ============================================================================
+ % POSTER CONFIGURATION
+ % ============================================================================
+
+ % Grid and columns
+ grid=false, % Set to true for debugging layout
+ columns=3, % Number of columns
+ colspacing=1.5em, % Space between columns
+
+ % Background
+ background=plain, % plain, shadetb, shadelr
+ bgColorOne=white,
+ bgColorTwo=white,
+
+ % Borders
+ borderColor=blue!50!black,
+ linewidth=2pt,
+
+ % Header
+ headerColorOne=blue!70!black,
+ headerColorTwo=blue!60!black,
+ headerFontColor=white,
+ headerheight=0.12\textheight,
+ headershape=roundedright, % rectangle, rounded, roundedright, roundedleft
+ headershade=plain, % plain, shadetb, shadelr
+ headerborder=closed, % open, closed
+ headerfont=\Large\sf\bf,
+
+ % Boxes
+ boxColorOne=white,
+ boxColorTwo=blue!10,
+ boxshade=plain,
+ textborder=roundedleft, % none, rectangle, rounded, roundedleft, roundedright
+
+ % Eye catcher
+ eyecatcher=true
+}
+% ============================================================================
+% HEADER CONTENT
+% ============================================================================
+% Eye Catcher (Left Logo)
+{
+ \includegraphics[height=6em]{logo1.pdf}
+}
+% Title
+{
+ \sf\bf Your Research Title: Concise and Descriptive
+}
+% Authors
+{
+ \vspace{0.3em}
+ Author One\textsuperscript{1}, Author Two\textsuperscript{2}, \underline{Presenting Author}\textsuperscript{1}\\[0.3em]
+ {\small
+ \textsuperscript{1}Department, University Name, City, Country\\
+ \textsuperscript{2}Research Institute Name, City, Country}
+}
+% University Logo (Right)
+{
+ \includegraphics[height=6em]{logo2.pdf}
+}
+
+% ==============================================================================
+% LEFT COLUMN
+% ==============================================================================
+
+\headerbox{Introduction}{name=intro,column=0,row=0}{
+ \textbf{Background}
+
+ Brief context establishing the importance of your research area (1-2 sentences).
+
+ \vspace{0.3cm}
+
+ \textbf{Problem Statement}
+
+ What gap or challenge does your work address? (1-2 sentences)
+
+ \vspace{0.3cm}
+
+ \textbf{Objective}
+
+ Clear statement of your research goal (1 sentence).
+}
+
+\headerbox{Methods}{name=methods,column=0,below=intro}{
+ \textbf{Study Design}
+ \begin{itemize}
+ \item Experimental approach or study type
+ \item Sample: n = X participants/samples
+ \item Key procedures
+ \end{itemize}
+
+ \vspace{0.3cm}
+
+ \textbf{Analysis}
+ \begin{itemize}
+ \item Statistical methods
+ \item Software: R 4.3, Python 3.10
+ \item Significance: p < 0.05
+ \end{itemize}
+
+ \vspace{0.3cm}
+
+ \begin{center}
+ \includegraphics[width=0.9\linewidth]{methods_flowchart.pdf}
+ \end{center}
+}
+
+% ==============================================================================
+% MIDDLE COLUMN (SPANS 2 COLUMNS FOR LARGE RESULT)
+% ==============================================================================
+
+\headerbox{Results: Main Finding}{name=results1,column=1,row=0,span=2}{
+ Brief description of your primary result. What is the key observation?
+
+ \vspace{0.3cm}
+
+ \begin{center}
+ \includegraphics[width=0.95\linewidth]{figure1.pdf}
+ \end{center}
+
+ \textbf{Figure 1:} Descriptive caption explaining the main result. Include statistics (Mean ± SD, n=X, **p<0.01).
+}
+
+% ==============================================================================
+% MIDDLE COLUMN (CONTINUES BELOW)
+% ==============================================================================
+
+\headerbox{Results: Finding 2}{name=results2,column=1,below=results1}{
+ Brief description of second key result.
+
+ \begin{center}
+ \includegraphics[width=0.9\linewidth]{figure2.pdf}
+ \end{center}
+
+ \textbf{Figure 2:} Supporting result or comparison.
+}
+
+% ==============================================================================
+% RIGHT COLUMN
+% ==============================================================================
+
+\headerbox{Results: Finding 3}{name=results3,column=2,below=results1}{
+ Brief description of third result or validation.
+
+ \begin{center}
+ \includegraphics[width=0.9\linewidth]{figure3.pdf}
+ \end{center}
+
+ \textbf{Figure 3:} Additional finding.
+}
+
+% ==============================================================================
+% BOTTOM ROW (SPANS ALL COLUMNS)
+% ==============================================================================
+
+\headerbox{Conclusions}{name=conclusions,column=0,span=2,above=bottom}{
+ \begin{multicols}{2}
+ \textbf{Key Findings}
+ \begin{itemize}
+ \item Main conclusion 1 with significance
+ \item Main conclusion 2 with impact
+ \item Main conclusion 3 with implications
+ \end{itemize}
+
+ \vspace{0.3cm}
+
+ \textbf{Limitations}
+ \begin{itemize}
+ \item Study constraints
+ \item Interpretation context
+ \end{itemize}
+
+ \columnbreak
+
+ \textbf{Future Directions}
+ \begin{itemize}
+ \item Ongoing studies
+ \item Broader applications
+ \item Next research questions
+ \end{itemize}
+
+ \vspace{0.3cm}
+
+ \textbf{Clinical/Practical Implications}
+ \begin{itemize}
+ \item Real-world applications
+ \item Impact on practice
+ \end{itemize}
+ \end{multicols}
+}
+
+\headerbox{Scan for More}{name=qr,column=2,above=bottom}{
+ \begin{center}
+ \qrcode[height=4cm]{https://doi.org/10.1234/your-paper}\\
+ \vspace{0.3cm}
+ \small Full paper, code \& data
+ \end{center}
+}
+
+% ==============================================================================
+% FOOTER (FULL WIDTH AT BOTTOM)
+% ==============================================================================
+
+\headerbox{}{name=footer,column=0,span=3,above=bottom,below=conclusions}{
+ \footnotesize
+ \begin{multicols}{2}
+ \textbf{References}
+ \begin{enumerate}
+ \item Author A et al. (2023). Title. \textit{Journal}, 10(2), 123-145.
+ \item Author B et al. (2024). Title. \textit{Conference}.
+ \item Author C et al. (2022). Title. \textit{Journal}, 15(3), 456-478.
+ \end{enumerate}
+
+ \columnbreak
+
+ \textbf{Acknowledgments}
+
+ Funded by Grant Agency (Grant \#12345). Thanks to collaborators at Institution X.
+
+ \vspace{0.3cm}
+
+ \textbf{Contact:} presenter.email@university.edu | labname.university.edu
+ \end{multicols}
+}
+
+\end{poster}
+
+\end{document}
+
diff --git a/scientific-skills/latex-posters/assets/beamerposter_template.tex b/scientific-skills/latex-posters/assets/beamerposter_template.tex
new file mode 100644
index 0000000..43c9bd7
--- /dev/null
+++ b/scientific-skills/latex-posters/assets/beamerposter_template.tex
@@ -0,0 +1,244 @@
+% ==============================================================================
+% Research Poster Template - beamerposter
+% ==============================================================================
+% A professional academic poster template using beamerposter
+% Customize colors, content, and layout as needed
+% ==============================================================================
+
+\documentclass[final,t]{beamer}
+\usepackage[size=a0,scale=1.4,orientation=portrait]{beamerposter}
+\usetheme{Berlin}
+\usecolortheme{beaver}
+
+% Remove default margins for full page coverage
+\setbeamersize{text margin left=5mm, text margin right=5mm}
+\usepackage[margin=10mm]{geometry}
+
+% Remove navigation symbols
+\setbeamertemplate{navigation symbols}{}
+
+% Packages
+\usepackage{graphicx}
+\usepackage{amsmath,amssymb}
+\usepackage{booktabs}
+\usepackage{multicol}
+\usepackage{qrcode}
+\usepackage{hyperref}
+
+% Font configuration
+\setbeamerfont{title}{size=\VeryHuge,series=\bfseries}
+\setbeamerfont{author}{size=\Large}
+\setbeamerfont{institute}{size=\normalsize}
+\setbeamerfont{block title}{size=\huge,series=\bfseries}
+\setbeamerfont{block body}{size=\LARGE}
+
+% Custom colors (customize to match your institution)
+\definecolor{primarycolor}{RGB}{0,51,102} % Dark blue
+\definecolor{secondarycolor}{RGB}{204,0,0} % Red
+\definecolor{accentcolor}{RGB}{255,204,0} % Gold
+
+\setbeamercolor{structure}{fg=primarycolor}
+\setbeamercolor{block title}{bg=primarycolor,fg=white}
+\setbeamercolor{block body}{bg=primarycolor!10,fg=black}
+
+% ==============================================================================
+% POSTER CONTENT - CUSTOMIZE BELOW
+% ==============================================================================
+
+\title{Your Research Title: Concise and Descriptive}
+\author{Author One\textsuperscript{1}, Author Two\textsuperscript{2}, \underline{Presenting Author}\textsuperscript{1}}
+\institute{
+ \textsuperscript{1}Department, University Name\\
+ \textsuperscript{2}Research Institute Name
+}
+
+\begin{document}
+
+\begin{frame}[t]
+
+ % ============================================================================
+ % HEADER
+ % ============================================================================
+ \begin{block}{}
+ \begin{columns}[T]
+ \begin{column}{.15\linewidth}
+ % Left logo
+ \includegraphics[width=0.9\linewidth]{logo1.pdf}
+ \end{column}
+
+ \begin{column}{.7\linewidth}
+ \centering
+ \usebeamerfont{title}\inserttitle\\[0.5cm]
+ \usebeamerfont{author}\insertauthor\\[0.3cm]
+ \usebeamerfont{institute}\insertinstitute
+ \end{column}
+
+ \begin{column}{.15\linewidth}
+ % Right logo
+ \includegraphics[width=0.9\linewidth]{logo2.pdf}
+ \end{column}
+ \end{columns}
+ \end{block}
+
+ \vspace{1cm}
+
+ % ============================================================================
+ % MAIN CONTENT - 3 COLUMN LAYOUT
+ % ============================================================================
+
+ \begin{columns}[t]
+
+ % ==========================================================================
+ % LEFT COLUMN
+ % ==========================================================================
+ \begin{column}{.3\linewidth}
+
+ \begin{block}{Introduction}
+ \textbf{Background:} Brief context about your research area (1-2 sentences).
+
+ \vspace{0.5cm}
+
+ \textbf{Problem:} What gap or challenge does your work address? (1-2 sentences)
+
+ \vspace{0.5cm}
+
+ \textbf{Objective:} Clear statement of your research goal (1 sentence).
+ \end{block}
+
+ \vspace{1cm}
+
+ \begin{block}{Methods}
+ \textbf{Study Design:}
+ \begin{itemize}
+ \item Experimental approach or design
+ \item Sample size and population
+ \item Key procedures
+ \end{itemize}
+
+ \vspace{0.5cm}
+
+ \textbf{Analysis:}
+ \begin{itemize}
+ \item Statistical methods
+ \item Software/tools used
+ \item Validation approach
+ \end{itemize}
+
+ \vspace{0.5cm}
+
+ % Optional: Methods flowchart
+ \begin{center}
+ \includegraphics[width=0.9\linewidth]{methods_flowchart.pdf}
+ \end{center}
+ \end{block}
+
+ \end{column}
+
+ % ==========================================================================
+ % MIDDLE COLUMN
+ % ==========================================================================
+ \begin{column}{.3\linewidth}
+
+ \begin{block}{Results}
+ \textbf{Finding 1:} Brief description
+
+ \begin{center}
+ \includegraphics[width=0.95\linewidth]{figure1.pdf}
+ \small Figure 1: Descriptive caption with key statistics (n=X, p<0.01).
+ \end{center}
+
+ \vspace{1cm}
+
+ \textbf{Finding 2:} Brief description
+
+ \begin{center}
+ \includegraphics[width=0.95\linewidth]{figure2.pdf}
+ \small Figure 2: Another key result showing comparison or trend.
+ \end{center}
+ \end{block}
+
+ \end{column}
+
+ % ==========================================================================
+ % RIGHT COLUMN
+ % ==========================================================================
+ \begin{column}{.3\linewidth}
+
+ \begin{block}{Results (continued)}
+ \textbf{Finding 3:} Brief description
+
+ \begin{center}
+ \includegraphics[width=0.95\linewidth]{figure3.pdf}
+ \small Figure 3: Additional important result or validation.
+ \end{center}
+ \end{block}
+
+ \vspace{1cm}
+
+ \begin{block}{Conclusions}
+ \textbf{Key Findings:}
+ \begin{itemize}
+ \item Main conclusion 1 with impact
+ \item Main conclusion 2 with significance
+ \item Main conclusion 3 with implications
+ \end{itemize}
+
+ \vspace{0.5cm}
+
+ \textbf{Limitations:}
+ \begin{itemize}
+ \item Brief acknowledgment of constraints
+ \item Context for interpretation
+ \end{itemize}
+
+ \vspace{0.5cm}
+
+ \textbf{Future Directions:}
+ \begin{itemize}
+ \item Next steps or ongoing work
+ \item Broader applications
+ \end{itemize}
+ \end{block}
+
+ \end{column}
+
+ \end{columns}
+
+ \vspace{1cm}
+
+ % ============================================================================
+ % FOOTER
+ % ============================================================================
+
+ \begin{block}{}
+ \footnotesize
+ \begin{columns}[T]
+ \begin{column}{.75\linewidth}
+ \textbf{References}
+ \begin{enumerate}
+ \item Author A et al. (2023). Title. \textit{Journal}, 10(2), 123-145.
+ \item Author B et al. (2024). Title. \textit{Conference Proceedings}.
+ \item Author C et al. (2022). Title. \textit{Journal}, 15(3), 456-478.
+ \end{enumerate}
+
+ \vspace{0.3cm}
+
+ \textbf{Acknowledgments:} Funded by Grant Agency (Grant \#12345). Thanks to collaborators and facility staff.
+
+ \vspace{0.3cm}
+
+ \textbf{Contact:} presenter.email@university.edu | Lab Website: labname.university.edu
+ \end{column}
+
+ \begin{column}{.2\linewidth}
+ \centering
+ \qrcode[height=3.5cm]{https://doi.org/10.1234/your-paper}\\
+ \tiny Scan for full paper
+ \end{column}
+ \end{columns}
+ \end{block}
+
+\end{frame}
+
+\end{document}
+
diff --git a/scientific-skills/latex-posters/assets/poster_quality_checklist.md b/scientific-skills/latex-posters/assets/poster_quality_checklist.md
new file mode 100644
index 0000000..9338688
--- /dev/null
+++ b/scientific-skills/latex-posters/assets/poster_quality_checklist.md
@@ -0,0 +1,358 @@
+# Research Poster Quality Checklist
+
+Use this comprehensive checklist before printing or presenting your research poster.
+
+## Pre-Compilation Checks
+
+### Content Completeness
+- [ ] Title is concise and descriptive (10-15 words)
+- [ ] All author names spelled correctly
+- [ ] Affiliations complete and accurate
+- [ ] Contact email address included
+- [ ] All sections present: Introduction, Methods, Results, Conclusions
+- [ ] References cited (5-10 key citations)
+- [ ] Acknowledgments included (funding, collaborators)
+- [ ] No placeholder text remaining (TODO, Lorem ipsum, etc.)
+
+### Visual Content
+- [ ] All figures prepared and high resolution (300+ DPI)
+- [ ] Figure captions written and descriptive
+- [ ] Logos available (university, funding agencies)
+- [ ] QR codes generated and tested
+- [ ] Icons/graphics sourced (if used)
+
+### LaTeX Configuration
+- [ ] Correct paper size specified (A0, A1, 36×48", etc.)
+- [ ] Correct orientation (portrait/landscape)
+- [ ] Minimal margins configured (5-15mm)
+- [ ] Font sizes appropriate (title 72pt+, body 24pt+)
+- [ ] Color scheme defined
+- [ ] All packages installed and working
+
+## Compilation Checks
+
+### Successful Compilation
+- [ ] PDF compiles without errors
+- [ ] No critical warnings in .log file
+- [ ] All citations resolved (no [?] marks)
+- [ ] All cross-references working
+- [ ] Bibliography generated correctly (if using BibTeX)
+
+### Warning Review
+Run in terminal: `grep -i "warning\|overfull\|underfull" poster.log`
+
+- [ ] No overfull hbox warnings (text too wide)
+- [ ] No underfull hbox warnings (excessive spacing)
+- [ ] No missing figure warnings
+- [ ] No missing font warnings
+- [ ] No undefined reference warnings
+
+## PDF Quality Checks
+
+### Automated Checks
+
+Run: `./scripts/review_poster.sh poster.pdf` or manually verify:
+
+#### Page Specifications
+```bash
+pdfinfo poster.pdf | grep "Page size"
+```
+- [ ] Page size matches requirements exactly
+- [ ] Single page document (not multi-page)
+- [ ] Correct orientation
+
+#### Font Embedding
+```bash
+pdffonts poster.pdf
+```
+- [ ] All fonts show "yes" in "emb" column
+- [ ] No bitmap fonts (should be Type 1 or TrueType)
+
+#### Image Quality
+```bash
+pdfimages -list poster.pdf
+```
+- [ ] All images at least 300 DPI
+- [ ] No JPEG artifacts in figures
+- [ ] Vector graphics used where possible
+
+#### File Size
+```bash
+ls -lh poster.pdf
+```
+- [ ] Reasonable size (2-50 MB typical)
+- [ ] Not too large for email (<50 MB) if sharing digitally
+- [ ] Not suspiciously small (<1 MB - may indicate low quality)
+
+## Visual Inspection (100% Zoom)
+
+### Layout and Spacing
+- [ ] Content fills entire page (no excessive white margins)
+- [ ] Consistent spacing between columns (1-2cm)
+- [ ] Consistent spacing between blocks (1-2cm)
+- [ ] All elements aligned to grid
+- [ ] No overlapping text or figures
+- [ ] White space evenly distributed (30-40% total)
+- [ ] Visual balance across poster (no heavy/empty areas)
+
+### Typography
+- [ ] Title readable and prominent (72-120pt)
+- [ ] Section headers clear (48-72pt)
+- [ ] Body text large enough (24-36pt minimum, 30pt+ recommended)
+- [ ] Captions readable (18-24pt)
+- [ ] No text running off edges
+- [ ] Consistent font usage throughout
+- [ ] Line spacing adequate (1.2-1.5×)
+- [ ] No awkward hyphenation or word breaks
+- [ ] All special characters render correctly (Greek, math symbols)
+
+### Visual Elements
+- [ ] All figures display correctly
+- [ ] No pixelated or blurry images
+- [ ] Figure resolution high (zoom to 200% to verify)
+- [ ] Figure labels large and clear
+- [ ] Graph axes labeled with units
+- [ ] Color schemes consistent across figures
+- [ ] Legends readable and well-positioned
+- [ ] Logos crisp and professional
+- [ ] QR codes sharp and high-contrast (minimum 2×2cm)
+- [ ] No visual artifacts or rendering errors
+
+### Colors
+- [ ] Colors render as intended (not washed out)
+- [ ] High contrast between text and background (≥4.5:1)
+- [ ] Color scheme harmonious
+- [ ] Colors appropriate for printing (not too bright/neon)
+- [ ] Institutional colors used correctly
+- [ ] Color-blind friendly palette (avoid red-green only)
+
+### Content
+- [ ] Title complete and correctly positioned
+- [ ] All author names and affiliations visible
+- [ ] All sections present and labeled
+- [ ] Results section has figures/data
+- [ ] Conclusions clearly stated
+- [ ] References formatted consistently
+- [ ] Contact information clearly visible
+- [ ] No missing content
+
+## Reduced-Scale Print Test (CRITICAL)
+
+### Test Print Preparation
+Print poster at 25% scale:
+- A0 poster → Print on A4 paper
+- 36×48" poster → Print on Letter paper
+- A1 poster → Print on A5 paper
+
+### Readability from Distance
+
+**From 6 feet (2 meters):**
+- [ ] Title clearly readable
+- [ ] Authors identifiable
+- [ ] Main figures visible
+
+**From 4 feet (1.2 meters):**
+- [ ] Section headers readable
+- [ ] Figure captions readable
+- [ ] Key results visible
+
+**From 2 feet (0.6 meters):**
+- [ ] Body text readable
+- [ ] References readable
+- [ ] All details clear
+
+### Print Quality
+- [ ] Colors accurate (match screen expectations)
+- [ ] No banding or color shifts
+- [ ] Sharp edges (not blurry)
+- [ ] Consistent print density
+- [ ] No printer artifacts
+
+## Content Proofreading
+
+### Text Accuracy
+- [ ] Spell-checked all text
+- [ ] Grammar checked
+- [ ] All author names spelled correctly
+- [ ] All affiliations accurate
+- [ ] Email address correct
+- [ ] No typos in title or headers
+
+### Scientific Accuracy
+- [ ] All numbers and statistics verified
+- [ ] Units included and correct
+- [ ] Statistical significance correctly indicated
+- [ ] Sample sizes (n=) reported
+- [ ] Figure numbering consistent
+- [ ] Citations accurate and complete
+- [ ] Methodology accurately described
+- [ ] Results match figures/data
+- [ ] Conclusions supported by data
+
+### Consistency
+- [ ] Terminology consistent throughout
+- [ ] Abbreviations defined at first use
+- [ ] Consistent notation (italics for genes, etc.)
+- [ ] Consistent units (don't mix metric/imperial)
+- [ ] Consistent decimal places
+- [ ] Consistent citation format
+
+## Accessibility Checks
+
+### Color Contrast
+Test at: https://webaim.org/resources/contrastchecker/
+
+- [ ] Title-background contrast ≥ 7:1
+- [ ] Body text-background contrast ≥ 4.5:1
+- [ ] All text meets WCAG AA standard minimum
+
+### Color Blindness
+Test with simulator: https://www.color-blindness.com/coblis-color-blindness-simulator/
+
+- [ ] Information not lost with deuteranopia (red-green)
+- [ ] Key distinctions visible with protanopia
+- [ ] Patterns/shapes used in addition to color
+- [ ] No critical info conveyed by color alone
+
+### Visual Clarity
+- [ ] Clear visual hierarchy (size, weight, position)
+- [ ] Logical reading order
+- [ ] Grouping of related elements obvious
+- [ ] Important info emphasized appropriately
+
+## Peer Review
+
+### 30-Second Test
+Show poster to colleague for 30 seconds, then ask:
+- [ ] They can identify the research topic
+- [ ] They can state the main finding
+- [ ] They remember the key figure
+
+### 5-Minute Review
+Ask colleague to read poster (5 minutes), then ask:
+- [ ] They understand the research question
+- [ ] They can explain the approach
+- [ ] They can summarize the conclusions
+- [ ] They identify what makes it novel/important
+
+### Feedback
+- [ ] Noted any confusing elements
+- [ ] Identified any unclear figures
+- [ ] Checked for jargon that needs definition
+- [ ] Verified logical flow
+
+## Pre-Printing Final Checks
+
+### Technical Specifications
+- [ ] PDF size exactly matches conference requirements
+- [ ] Orientation correct (portrait vs landscape)
+- [ ] All fonts embedded (verified with pdffonts)
+- [ ] Color space correct (RGB for screen, CMYK if printer requires)
+- [ ] Resolution adequate (300+ DPI for all images)
+- [ ] Bleed area added if required (typically 3-5mm)
+- [ ] Crop marks visible if required
+- [ ] File naming convention followed
+
+### Printer Communication
+- [ ] Confirmed paper type (matte vs glossy)
+- [ ] Confirmed poster size
+- [ ] Provided color profile if required
+- [ ] Verified delivery deadline
+- [ ] Confirmed shipping/pickup arrangements
+- [ ] Discussed backup plan if issues arise
+
+### Backup and Storage
+- [ ] PDF saved with clear filename: `LastName_Conference_Poster.pdf`
+- [ ] Source .tex file backed up
+- [ ] All figure files backed up
+- [ ] Copy saved to cloud storage
+- [ ] Copy saved on USB drive for conference
+- [ ] Digital version ready to email if requested
+
+## Digital Presentation Checks
+
+If presenting digitally or sharing online:
+
+### File Optimization
+- [ ] PDF compressed if >10MB (for email)
+- [ ] Test opens in Adobe Reader
+- [ ] Test opens in Preview (Mac)
+- [ ] Test opens in browser PDF viewers
+- [ ] Test on mobile devices
+
+### Interactive Elements
+- [ ] All QR codes tested and functional
+- [ ] QR codes link to correct URLs
+- [ ] Hyperlinks work (if included)
+- [ ] Links open in new tabs/windows appropriately
+
+### Alternative Formats
+- [ ] PNG version created for social media (if needed)
+- [ ] Thumbnail image created
+- [ ] Poster description/abstract prepared
+- [ ] Hashtags and social media text ready
+
+## Conference-Specific
+
+### Requirements Verification
+- [ ] Poster size matches conference specifications exactly
+- [ ] Orientation matches requirements
+- [ ] File format correct (usually PDF)
+- [ ] Submission deadline met
+- [ ] File naming convention followed
+- [ ] Abstract/description submitted if required
+
+### Physical Preparation
+- [ ] Poster printed and inspected
+- [ ] Backup printed copy prepared
+- [ ] Push pins/mounting materials ready
+- [ ] Poster tube or flat portfolio for transport
+- [ ] Business cards/handouts prepared
+- [ ] Digital backup on laptop/phone
+
+### Presentation Preparation
+- [ ] 30-second elevator pitch prepared
+- [ ] 2-minute summary prepared
+- [ ] 5-minute detailed explanation prepared
+- [ ] Anticipated questions considered
+- [ ] Follow-up materials ready (QR code to paper, etc.)
+
+## Final Sign-Off
+
+Date: ________________
+
+Poster Title: _______________________________________________
+
+Conference: _______________________________________________
+
+Reviewed by: _______________________________________________
+
+All critical items checked: [ ]
+
+Ready for printing: [ ]
+
+Ready for presentation: [ ]
+
+Notes/Issues to address:
+_________________________________________________________
+_________________________________________________________
+_________________________________________________________
+
+---
+
+## Quick Reference: Common Issues
+
+| Issue | Quick Fix |
+|-------|-----------|
+| Large white margins | Reduce margin in documentclass: `margin=5mm` |
+| Text too small | Increase scale: `scale=1.5` in beamerposter |
+| Blurry figures | Use vector graphics (PDF) or higher resolution (600+ DPI) |
+| Colors wrong | Check RGB vs CMYK, test print before final |
+| Fonts not embedded | Compile with: `pdflatex -dEmbedAllFonts=true` |
+| Content cut off | Check total width: columns + spacing + margins = pagewidth |
+| QR codes don't scan | Increase size (min 2×2cm), ensure high contrast |
+| File too large | Compress: `gs -sDEVICE=pdfwrite -dPDFSETTINGS=/printer ...` |
+
+## Checklist Version
+Version 1.0 - For use with LaTeX poster packages (beamerposter, tikzposter, baposter)
+
diff --git a/scientific-skills/latex-posters/assets/tikzposter_template.tex b/scientific-skills/latex-posters/assets/tikzposter_template.tex
new file mode 100644
index 0000000..6247188
--- /dev/null
+++ b/scientific-skills/latex-posters/assets/tikzposter_template.tex
@@ -0,0 +1,251 @@
+% ==============================================================================
+% Research Poster Template - tikzposter
+% ==============================================================================
+% A modern, colorful poster template using tikzposter
+% Customize themes, colors, and content as needed
+% ==============================================================================
+
+\documentclass[
+ 25pt, % Font scaling
+ a0paper, % Paper size
+ portrait, % Orientation
+ margin=10mm, % Outer margins (minimal for full page)
+ innermargin=15mm, % Space inside blocks
+ blockverticalspace=15mm, % Space between blocks
+ colspace=15mm, % Space between columns
+ subcolspace=8mm % Space between subcolumns
+]{tikzposter}
+
+% Packages
+\usepackage{graphicx}
+\usepackage{amsmath,amssymb}
+\usepackage{booktabs}
+\usepackage{qrcode}
+\usepackage{hyperref}
+
+% Theme selection (uncomment your choice)
+\usetheme{Rays} % Modern with radiating background
+% \usetheme{Wave} % Clean with decorative wave
+% \usetheme{Board} % Board-style with texture
+% \usetheme{Envelope} % Minimal with envelope corners
+% \usetheme{Default} % Professional with lines
+
+% Color style (uncomment your choice)
+\usecolorstyle{Denmark} % Professional blue
+% \usecolorstyle{Australia} % Warm colors
+% \usecolorstyle{Sweden} % Cool tones
+% \usecolorstyle{Britain} % Earth tones
+
+% Custom color scheme (optional - comment out if using built-in)
+% \definecolorstyle{CustomStyle}{
+% \definecolor{colorOne}{RGB}{0,51,102} % Dark blue
+% \definecolor{colorTwo}{RGB}{255,204,0} % Gold
+% \definecolor{colorThree}{RGB}{204,0,0} % Red
+% }{
+% % Background Colors
+% \colorlet{backgroundcolor}{white}
+% \colorlet{framecolor}{colorOne}
+% % Title Colors
+% \colorlet{titlefgcolor}{white}
+% \colorlet{titlebgcolor}{colorOne}
+% % Block Colors
+% \colorlet{blocktitlebgcolor}{colorOne}
+% \colorlet{blocktitlefgcolor}{white}
+% \colorlet{blockbodybgcolor}{white}
+% \colorlet{blockbodyfgcolor}{black}
+% }
+% \usecolorstyle{CustomStyle}
+
+% ==============================================================================
+% POSTER CONTENT - CUSTOMIZE BELOW
+% ==============================================================================
+
+\title{Your Research Title: Concise and Descriptive}
+\author{Author One\textsuperscript{1}, Author Two\textsuperscript{2}, \underline{Presenting Author}\textsuperscript{1}}
+\institute{
+ \textsuperscript{1}Department, University Name, City, Country\\
+ \textsuperscript{2}Research Institute Name, City, Country
+}
+
+% Title matter (logos)
+\titlegraphic{
+ \includegraphics[width=0.1\textwidth]{logo1.pdf}
+ \hspace{3cm}
+ \includegraphics[width=0.1\textwidth]{logo2.pdf}
+}
+
+\begin{document}
+
+\maketitle
+
+% ==============================================================================
+% MAIN CONTENT - 3 COLUMN LAYOUT
+% ==============================================================================
+
+\begin{columns}
+
+ % ============================================================================
+ % LEFT COLUMN
+ % ============================================================================
+ \column{0.33}
+
+ \block{Introduction}{
+ \textbf{Background}
+
+ Brief context about your research area. One to two sentences establishing the importance of the topic.
+
+ \vspace{0.5cm}
+
+ \textbf{Problem Statement}
+
+ What gap or challenge does your work address? Why is this important? One to two sentences.
+
+ \vspace{0.5cm}
+
+ \textbf{Research Objective}
+
+ Clear, concise statement of what you set out to do in this study.
+ }
+
+ \block{Methods}{
+ \textbf{Study Design}
+ \begin{itemize}
+ \item Experimental approach or study type
+ \item Sample size: n = X participants/samples
+ \item Key inclusion/exclusion criteria
+ \end{itemize}
+
+ \vspace{0.5cm}
+
+ \textbf{Procedures}
+ \begin{itemize}
+ \item Main experimental steps
+ \item Key measurements or interventions
+ \item Data collection approach
+ \end{itemize}
+
+ \vspace{0.5cm}
+
+ \textbf{Analysis}
+ \begin{itemize}
+ \item Statistical methods used
+ \item Software/tools (e.g., R 4.3, Python)
+ \item Significance threshold (p < 0.05)
+ \end{itemize}
+
+ \vspace{0.5cm}
+
+ % Optional: Methods flowchart
+ \begin{tikzfigure}
+ \includegraphics[width=0.9\linewidth]{methods_diagram.pdf}
+ \end{tikzfigure}
+ }
+
+ % ============================================================================
+ % MIDDLE COLUMN
+ % ============================================================================
+ \column{0.33}
+
+ \block{Results: Finding 1}{
+ Brief description of your first main result. What did you observe?
+
+ \begin{tikzfigure}
+ \includegraphics[width=0.95\linewidth]{figure1.pdf}
+ \end{tikzfigure}
+
+ \textbf{Figure 1:} Descriptive caption explaining the figure. Include key statistics (Mean ± SD, n=X, **p<0.01).
+ }
+
+ \block{Results: Finding 2}{
+ Brief description of your second main result.
+
+ \begin{tikzfigure}
+ \includegraphics[width=0.95\linewidth]{figure2.pdf}
+ \end{tikzfigure}
+
+ \textbf{Figure 2:} Another key result showing comparison, trend, or correlation.
+ }
+
+ % ============================================================================
+ % RIGHT COLUMN
+ % ============================================================================
+ \column{0.33}
+
+ \block{Results: Finding 3}{
+ Brief description of your third main result or validation.
+
+ \begin{tikzfigure}
+ \includegraphics[width=0.95\linewidth]{figure3.pdf}
+ \end{tikzfigure}
+
+ \textbf{Figure 3:} Additional important finding or supporting data.
+ }
+
+ \block{Conclusions}{
+ \textbf{Key Findings}
+ \begin{itemize}
+ \item \textbf{Main conclusion 1:} Impact and significance
+ \item \textbf{Main conclusion 2:} Novel contribution
+ \item \textbf{Main conclusion 3:} Practical implications
+ \end{itemize}
+
+ \vspace{0.5cm}
+
+ \textbf{Limitations}
+ \begin{itemize}
+ \item Brief acknowledgment of study constraints
+ \item Context for result interpretation
+ \end{itemize}
+
+ \vspace{0.5cm}
+
+ \textbf{Future Directions}
+ \begin{itemize}
+ \item Ongoing or planned follow-up studies
+ \item Broader applications of findings
+ \end{itemize}
+ }
+
+ \block{Scan for More}{
+ \begin{center}
+ \qrcode[height=5cm]{https://doi.org/10.1234/your-paper}\\
+ \vspace{0.5cm}
+ \large Full paper, code, and data
+ \end{center}
+ }
+
+\end{columns}
+
+% ==============================================================================
+% FOOTER (Full Width)
+% ==============================================================================
+
+\block[width=1.0\linewidth]{}{
+ \footnotesize
+ \begin{minipage}{0.7\textwidth}
+ \textbf{References}
+ \begin{enumerate}
+ \item Author A et al. (2023). Title of paper. \textit{Journal Name}, 10(2), 123-145. doi:10.xxxx/xxxxx
+ \item Author B et al. (2024). Title of paper. \textit{Conference Proceedings}.
+ \item Author C et al. (2022). Title of paper. \textit{Journal Name}, 15(3), 456-478.
+ \end{enumerate}
+
+ \vspace{0.3cm}
+
+ \textbf{Acknowledgments:} This work was supported by Funding Agency (Grant \#12345). We thank collaborators at Institution X and the Core Facility for technical support.
+
+ \vspace{0.3cm}
+
+ \textbf{Contact:} presenter.email@university.edu | Twitter: @labname | Website: labname.university.edu
+ \end{minipage}%
+ \hfill
+ \begin{minipage}{0.25\textwidth}
+ \raggedleft
+ Conference Name 2024\\
+ Location, Dates\\
+ Poster \#XXX
+ \end{minipage}
+}
+
+\end{document}
+
diff --git a/scientific-skills/latex-posters/references/latex_poster_packages.md b/scientific-skills/latex-posters/references/latex_poster_packages.md
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+# LaTeX Poster Packages: Comprehensive Comparison
+
+## Overview
+
+Three major LaTeX packages dominate research poster creation: beamerposter, tikzposter, and baposter. Each has distinct strengths, syntax, and use cases. This guide provides detailed comparisons and practical examples.
+
+## Package Comparison Matrix
+
+| Feature | beamerposter | tikzposter | baposter |
+|---------|--------------|------------|----------|
+| **Learning Curve** | Easy (if familiar with Beamer) | Moderate | Moderate |
+| **Flexibility** | Moderate | High | Moderate-High |
+| **Default Aesthetics** | Traditional/Academic | Modern/Colorful | Professional/Clean |
+| **Theme Support** | Extensive (Beamer themes) | Built-in + Custom | Limited built-in |
+| **Customization** | Moderate effort | Easy with TikZ | Structured approach |
+| **Layout System** | Frame-based | Block-based | Box-based with grid |
+| **Multi-column** | Manual | Automatic | Automatic |
+| **Graphics Integration** | Standard includegraphics | TikZ + includegraphics | Standard + advanced |
+| **Community Support** | Large (Beamer community) | Growing | Smaller |
+| **Best For** | Traditional academic, institutional branding | Creative designs, custom graphics | Structured multi-column layouts |
+| **File Size** | Small | Medium-Large (TikZ overhead) | Medium |
+| **Compilation Speed** | Fast | Slower (TikZ processing) | Fast-Medium |
+
+## 1. beamerposter
+
+### Overview
+
+beamerposter extends the popular Beamer presentation class for poster-sized documents. It inherits all Beamer functionality, themes, and customization options.
+
+### Advantages
+
+- **Familiar syntax**: If you know Beamer, you know beamerposter
+- **Extensive themes**: Access to all Beamer themes and color schemes
+- **Institutional branding**: Easy to match university templates
+- **Stable and mature**: Well-tested, extensive documentation
+- **Block structure**: Clear organizational units
+- **Good for traditional posters**: Academic conferences, thesis defenses
+
+### Disadvantages
+
+- **Less flexible layouts**: Column-based system can be restrictive
+- **Manual positioning**: Requires careful spacing adjustments
+- **Traditional aesthetics**: Can look dated compared to modern designs
+- **Limited built-in styling**: Requires theme customization for unique looks
+
+### Basic Template
+
+```latex
+\documentclass[final,t]{beamer}
+\usepackage[size=a0,scale=1.4,orientation=portrait]{beamerposter}
+\usetheme{Berlin}
+\usecolortheme{beaver}
+
+% Configure fonts
+\setbeamerfont{title}{size=\VeryHuge,series=\bfseries}
+\setbeamerfont{author}{size=\Large}
+\setbeamerfont{block title}{size=\large,series=\bfseries}
+
+\title{Your Research Title}
+\author{Author Names}
+\institute{Institution}
+
+\begin{document}
+\begin{frame}[t]
+
+ % Title block
+ \begin{block}{}
+ \maketitle
+ \end{block}
+
+ \begin{columns}[t]
+ \begin{column}{.45\linewidth}
+
+ \begin{block}{Introduction}
+ Your introduction text here...
+ \end{block}
+
+ \begin{block}{Methods}
+ Your methods text here...
+ \end{block}
+
+ \end{column}
+
+ \begin{column}{.45\linewidth}
+
+ \begin{block}{Results}
+ Your results text here...
+ \includegraphics[width=\linewidth]{figure.pdf}
+ \end{block}
+
+ \begin{block}{Conclusions}
+ Your conclusions here...
+ \end{block}
+
+ \end{column}
+ \end{columns}
+
+\end{frame}
+\end{document}
+```
+
+### Popular Themes
+
+```latex
+% Traditional academic
+\usetheme{Berlin}
+\usecolortheme{beaver}
+
+% Modern minimal
+\usetheme{Madrid}
+\usecolortheme{whale}
+
+% Blue professional
+\usetheme{Singapore}
+\usecolortheme{dolphin}
+
+% Dark theme
+\usetheme{Warsaw}
+\usecolortheme{seahorse}
+```
+
+### Custom Colors
+
+```latex
+% Define custom colors
+\definecolor{primarycolor}{RGB}{0,51,102} % Dark blue
+\definecolor{secondarycolor}{RGB}{204,0,0} % Red
+\definecolor{accentcolor}{RGB}{255,204,0} % Gold
+
+% Apply to beamer elements
+\setbeamercolor{structure}{fg=primarycolor}
+\setbeamercolor{block title}{bg=primarycolor,fg=white}
+\setbeamercolor{block body}{bg=primarycolor!10,fg=black}
+```
+
+### Advanced Customization
+
+```latex
+% Remove navigation symbols
+\setbeamertemplate{navigation symbols}{}
+
+% Custom title formatting
+\setbeamertemplate{title page}{
+ \begin{center}
+ {\usebeamerfont{title}\usebeamercolor[fg]{title}\inserttitle}\\[1cm]
+ {\usebeamerfont{author}\insertauthor}\\[0.5cm]
+ {\usebeamerfont{institute}\insertinstitute}
+ \end{center}
+}
+
+% Custom block style
+\setbeamertemplate{block begin}{
+ \par\vskip\medskipamount
+ \begin{beamercolorbox}[colsep*=.75ex,rounded=true]{block title}
+ \usebeamerfont*{block title}\insertblocktitle
+ \end{beamercolorbox}
+ {\parskip0pt\par}
+ \usebeamerfont{block body}
+ \begin{beamercolorbox}[colsep*=.75ex,vmode,rounded=true]{block body}
+}
+```
+
+### Three-Column Layout
+
+```latex
+\begin{columns}[t]
+ \begin{column}{.3\linewidth}
+ % Left column content
+ \end{column}
+ \begin{column}{.3\linewidth}
+ % Middle column content
+ \end{column}
+ \begin{column}{.3\linewidth}
+ % Right column content
+ \end{column}
+\end{columns}
+```
+
+## 2. tikzposter
+
+### Overview
+
+tikzposter is built on the powerful TikZ graphics package, offering modern designs with extensive customization through TikZ commands.
+
+### Advantages
+
+- **Modern aesthetics**: Contemporary, colorful designs out-of-the-box
+- **Flexible block placement**: Easy positioning anywhere on poster
+- **Beautiful themes**: Multiple professionally designed themes included
+- **TikZ integration**: Seamless graphics and custom drawings
+- **Color customization**: Easy to create custom color palettes
+- **Automatic spacing**: Intelligent block spacing and alignment
+
+### Disadvantages
+
+- **Compilation time**: TikZ processing can be slow for large posters
+- **File size**: PDFs can be larger due to TikZ elements
+- **Learning curve**: TikZ syntax can be complex for advanced customization
+- **Less institutional theme support**: Requires more work to match branding
+
+### Basic Template
+
+```latex
+\documentclass[25pt, a0paper, portrait, margin=0mm, innermargin=15mm,
+ blockverticalspace=15mm, colspace=15mm, subcolspace=8mm]{tikzposter}
+
+\title{Your Research Title}
+\author{Author Names}
+\institute{Institution}
+
+% Choose theme and color style
+\usetheme{Rays}
+\usecolorstyle{Denmark}
+
+\begin{document}
+
+\maketitle
+
+% First column
+\begin{columns}
+ \column{0.5}
+
+ \block{Introduction}{
+ Your introduction text here...
+ }
+
+ \block{Methods}{
+ Your methods text here...
+ }
+
+ % Second column
+ \column{0.5}
+
+ \block{Results}{
+ Your results text here...
+ \begin{tikzfigure}
+ \includegraphics[width=0.9\linewidth]{figure.pdf}
+ \end{tikzfigure}
+ }
+
+ \block{Conclusions}{
+ Your conclusions here...
+ }
+
+\end{columns}
+
+\end{document}
+```
+
+### Available Themes
+
+```latex
+% Modern with radiating background
+\usetheme{Rays}
+
+% Clean with decorative wave
+\usetheme{Wave}
+
+% Minimal with envelope corners
+\usetheme{Envelope}
+
+% Traditional academic
+\usetheme{Basic}
+
+% Board-style with texture
+\usetheme{Board}
+
+% Clean minimal
+\usetheme{Simple}
+
+% Professional with lines
+\usetheme{Default}
+
+% Autumn color scheme
+\usetheme{Autumn}
+
+% Desert color palette
+\usetheme{Desert}
+```
+
+### Color Styles
+
+```latex
+% Professional blue
+\usecolorstyle{Denmark}
+
+% Warm colors
+\usecolorstyle{Australia}
+
+% Cool tones
+\usecolorstyle{Sweden}
+
+% Earth tones
+\usecolorstyle{Britain}
+
+% Default color scheme
+\usecolorstyle{Default}
+```
+
+### Custom Color Definition
+
+```latex
+\definecolorstyle{CustomStyle}{
+ \definecolor{colorOne}{RGB}{0,51,102} % Dark blue
+ \definecolor{colorTwo}{RGB}{255,204,0} % Gold
+ \definecolor{colorThree}{RGB}{204,0,0} % Red
+}{
+ % Background Colors
+ \colorlet{backgroundcolor}{white}
+ \colorlet{framecolor}{colorOne}
+ % Title Colors
+ \colorlet{titlefgcolor}{white}
+ \colorlet{titlebgcolor}{colorOne}
+ % Block Colors
+ \colorlet{blocktitlebgcolor}{colorOne}
+ \colorlet{blocktitlefgcolor}{white}
+ \colorlet{blockbodybgcolor}{white}
+ \colorlet{blockbodyfgcolor}{black}
+ % Innerblock Colors
+ \colorlet{innerblocktitlebgcolor}{colorTwo}
+ \colorlet{innerblocktitlefgcolor}{black}
+ \colorlet{innerblockbodybgcolor}{colorTwo!10}
+ \colorlet{innerblockbodyfgcolor}{black}
+ % Note colors
+ \colorlet{notefgcolor}{black}
+ \colorlet{notebgcolor}{colorThree!20}
+}
+
+\usecolorstyle{CustomStyle}
+```
+
+### Block Placement and Sizing
+
+```latex
+% Full-width block
+\block{Title}{Content}
+
+% Specify width
+\block[width=0.8\linewidth]{Title}{Content}
+
+% Position manually
+\block[x=10, y=50, width=30]{Title}{Content}
+
+% Inner blocks (nested, different styling)
+\block{Outer Title}{
+ \innerblock{Inner Title}{
+ Highlighted content
+ }
+}
+
+% Note blocks (for emphasis)
+\note[width=0.4\linewidth]{
+ Important note text
+}
+```
+
+### Advanced Features
+
+```latex
+% QR codes with tikzposter styling
+\block{Scan for More}{
+ \begin{center}
+ \qrcode[height=5cm]{https://github.com/project}\\
+ \vspace{0.5cm}
+ Visit our GitHub repository
+ \end{center}
+}
+
+% Multi-column within block
+\block{Results}{
+ \begin{tabular}{cc}
+ \includegraphics[width=0.45\linewidth]{fig1.pdf} &
+ \includegraphics[width=0.45\linewidth]{fig2.pdf}
+ \end{tabular}
+}
+
+% Custom TikZ graphics
+\block{Methodology}{
+ \begin{tikzpicture}
+ \node[draw, rectangle, fill=blue!20] (A) {Step 1};
+ \node[draw, rectangle, fill=green!20, right=of A] (B) {Step 2};
+ \draw[->, thick] (A) -- (B);
+ \end{tikzpicture}
+}
+```
+
+## 3. baposter
+
+### Overview
+
+baposter (Box Area Poster) uses a box-based layout system with automatic positioning and spacing. Excellent for structured, professional multi-column layouts.
+
+### Advantages
+
+- **Automatic layout**: Intelligent box positioning and spacing
+- **Professional defaults**: Clean, polished appearance out-of-the-box
+- **Multi-column excellence**: Best-in-class column-based layouts
+- **Header/footer boxes**: Easy institutional branding
+- **Consistent spacing**: Automatic vertical and horizontal alignment
+- **Print-ready**: Excellent CMYK support
+
+### Disadvantages
+
+- **Less flexible**: Box-based system can be constraining
+- **Fewer themes**: Limited built-in theme options
+- **Learning curve**: Unique syntax requires time to master
+- **Less active development**: Smaller community compared to others
+
+### Basic Template
+
+```latex
+\documentclass[a0paper,portrait]{baposter}
+
+\usepackage{graphicx}
+\usepackage{multicol}
+
+\begin{document}
+
+\begin{poster}{
+ % Options
+ grid=false,
+ columns=3,
+ colspacing=1em,
+ bgColorOne=white,
+ bgColorTwo=white,
+ borderColor=blue!50,
+ headerColorOne=blue!80,
+ headerColorTwo=blue!70,
+ headerFontColor=white,
+ boxColorOne=white,
+ boxColorTwo=blue!10,
+ textborder=roundedleft,
+ eyecatcher=true,
+ headerborder=open,
+ headerheight=0.12\textheight,
+ headershape=roundedright,
+ headershade=plain,
+ headerfont=\Large\sf\bf,
+ linewidth=2pt
+}
+% Eye Catcher (Logo)
+{
+ \includegraphics[height=6em]{logo.pdf}
+}
+% Title
+{
+ Your Research Title
+}
+% Authors
+{
+ Author Names\\
+ Institution Name
+}
+% University Logo
+{
+ \includegraphics[height=6em]{university-logo.pdf}
+}
+
+% First column boxes
+\headerbox{Introduction}{name=intro,column=0,row=0}{
+ Your introduction text here...
+}
+
+\headerbox{Methods}{name=methods,column=0,below=intro}{
+ Your methods text here...
+}
+
+% Second column boxes
+\headerbox{Results}{name=results,column=1,row=0,span=2}{
+ Your results here...
+ \includegraphics[width=0.9\linewidth]{results.pdf}
+}
+
+\headerbox{Analysis}{name=analysis,column=1,below=results}{
+ Analysis details...
+}
+
+\headerbox{Validation}{name=validation,column=2,below=results}{
+ Validation results...
+}
+
+% Bottom spanning box
+\headerbox{Conclusions}{name=conclusions,column=0,span=3,above=bottom}{
+ Your conclusions here...
+}
+
+\end{poster}
+\end{document}
+```
+
+### Box Positioning
+
+```latex
+% Position by column and row
+\headerbox{Title}{name=box1, column=0, row=0}{Content}
+
+% Position relative to other boxes
+\headerbox{Title}{name=box2, column=0, below=box1}{Content}
+
+% Above another box
+\headerbox{Title}{name=box3, column=1, above=bottom}{Content}
+
+% Span multiple columns
+\headerbox{Title}{name=box4, column=0, span=2, row=0}{Content}
+
+% Between two boxes vertically
+\headerbox{Title}{name=box5, column=0, below=box1, above=box3}{Content}
+
+% Aligned with another box
+\headerbox{Title}{name=box6, column=1, aligned=box1}{Content}
+```
+
+### Styling Options
+
+```latex
+\begin{poster}{
+ % Grid and layout
+ grid=false, % Show layout grid (debug)
+ columns=3, % Number of columns
+ colspacing=1em, % Space between columns
+
+ % Background
+ background=plain, % plain, shadetb, shadelr, user
+ bgColorOne=white,
+ bgColorTwo=lightgray,
+
+ % Borders
+ borderColor=blue!50,
+ linewidth=2pt,
+
+ % Header
+ headerColorOne=blue!80,
+ headerColorTwo=blue!70,
+ headerFontColor=white,
+ headerheight=0.12\textheight,
+ headershape=roundedright, % rectangle, rounded, roundedright, roundedleft
+ headershade=plain, % plain, shadetb, shadelr
+ headerborder=open, % open, closed
+
+ % Boxes
+ boxColorOne=white,
+ boxColorTwo=blue!10,
+ boxshade=plain, % plain, shadetb, shadelr
+ textborder=roundedleft, % none, rectangle, rounded, roundedleft, roundedright
+
+ % Eye catcher
+ eyecatcher=true
+}
+```
+
+### Color Schemes
+
+```latex
+% Professional blue
+\begin{poster}{
+ headerColorOne=blue!80,
+ headerColorTwo=blue!70,
+ boxColorTwo=blue!10,
+ borderColor=blue!50
+}
+
+% Academic green
+\begin{poster}{
+ headerColorOne=green!70!black,
+ headerColorTwo=green!60!black,
+ boxColorTwo=green!10,
+ borderColor=green!50
+}
+
+% Corporate gray
+\begin{poster}{
+ headerColorOne=gray!60,
+ headerColorTwo=gray!50,
+ boxColorTwo=gray!10,
+ borderColor=gray!40
+}
+```
+
+## Package Selection Guide
+
+### Choose beamerposter if:
+- ✅ You're already familiar with Beamer
+- ✅ You need to match institutional Beamer themes
+- ✅ You prefer traditional academic aesthetics
+- ✅ You want extensive theme options
+- ✅ You need fast compilation times
+- ✅ You're creating posters for conservative academic conferences
+
+### Choose tikzposter if:
+- ✅ You want modern, colorful designs
+- ✅ You plan to create custom graphics with TikZ
+- ✅ You value aesthetic flexibility
+- ✅ You want built-in professional themes
+- ✅ You don't mind slightly longer compilation
+- ✅ You're presenting at design-conscious or public-facing events
+
+### Choose baposter if:
+- ✅ You need structured multi-column layouts
+- ✅ You want automatic box positioning
+- ✅ You prefer clean, professional defaults
+- ✅ You need precise control over box relationships
+- ✅ You're creating posters with many sections
+- ✅ You value consistent spacing and alignment
+
+## Conversion Between Packages
+
+### From beamerposter to tikzposter
+
+```latex
+% beamerposter
+\begin{block}{Title}
+ Content
+\end{block}
+
+% tikzposter equivalent
+\block{Title}{
+ Content
+}
+```
+
+### From beamerposter to baposter
+
+```latex
+% beamerposter
+\begin{block}{Introduction}
+ Content
+\end{block}
+
+% baposter equivalent
+\headerbox{Introduction}{name=intro, column=0, row=0}{
+ Content
+}
+```
+
+### From tikzposter to baposter
+
+```latex
+% tikzposter
+\block{Methods}{
+ Content
+}
+
+% baposter equivalent
+\headerbox{Methods}{name=methods, column=0, row=0}{
+ Content
+}
+```
+
+## Compilation Tips
+
+### Faster Compilation
+
+```bash
+# Use draft mode for initial edits
+\documentclass[draft]{tikzposter}
+
+# Compile with faster engines when possible
+pdflatex -interaction=nonstopmode poster.tex
+
+# For tikzposter, use externalization to cache TikZ graphics
+\usetikzlibrary{external}
+\tikzexternalize
+```
+
+### Memory Issues
+
+```latex
+% Increase TeX memory for large posters
+% Add to poster preamble:
+\pdfminorversion=7
+\pdfobjcompresslevel=2
+```
+
+### Font Embedding
+
+```bash
+# Ensure fonts are embedded (required for printing)
+pdflatex -dEmbedAllFonts=true poster.tex
+
+# Check font embedding
+pdffonts poster.pdf
+```
+
+## Hybrid Approaches
+
+You can combine strengths of different packages:
+
+### beamerposter with TikZ Graphics
+
+```latex
+\documentclass[final]{beamer}
+\usepackage[size=a0]{beamerposter}
+\usepackage{tikz}
+
+\begin{block}{Flowchart}
+ \begin{tikzpicture}
+ % Custom TikZ graphics within beamerposter
+ \end{tikzpicture}
+\end{block}
+```
+
+### tikzposter with Beamer Themes
+
+```latex
+\documentclass{tikzposter}
+
+% Import specific Beamer color definitions
+\definecolor{beamerblue}{RGB}{0,51,102}
+\colorlet{blocktitlebgcolor}{beamerblue}
+```
+
+## Recommended Packages for All Systems
+
+```latex
+% Essential packages for any poster
+\usepackage{graphicx} % Images
+\usepackage{amsmath,amssymb} % Math symbols
+\usepackage{booktabs} % Professional tables
+\usepackage{multicol} % Multiple columns in text
+\usepackage{qrcode} % QR codes
+\usepackage{hyperref} % Hyperlinks
+\usepackage{caption} % Caption customization
+\usepackage{subcaption} % Subfigures
+```
+
+## Performance Comparison
+
+| Package | Compile Time (A0) | PDF Size | Memory Usage |
+|---------|-------------------|----------|--------------|
+| beamerposter | ~5-10 seconds | 2-5 MB | Low |
+| tikzposter | ~15-30 seconds | 5-15 MB | Medium-High |
+| baposter | ~8-15 seconds | 3-8 MB | Medium |
+
+*Note: Times for poster with 5 figures, typical conference content*
+
+## Conclusion
+
+All three packages are excellent choices for different scenarios:
+
+- **beamerposter**: Best for traditional academic settings and Beamer users
+- **tikzposter**: Best for modern, visually striking presentations
+- **baposter**: Best for structured, professional multi-section posters
+
+Choose based on your specific needs, aesthetic preferences, and time constraints. When in doubt, start with tikzposter for modern conferences or beamerposter for traditional academic venues.
+
diff --git a/scientific-skills/latex-posters/references/poster_content_guide.md b/scientific-skills/latex-posters/references/poster_content_guide.md
new file mode 100644
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+# Research Poster Content Guide
+
+## Overview
+
+Content is king in research posters. This guide covers writing strategies, section-specific guidance, visual-text balance, and best practices for communicating research effectively in poster format.
+
+## Core Content Principles
+
+### 1. The 3-5 Minute Rule
+
+**Reality**: Most viewers spend 3-5 minutes at your poster
+- **1 minute**: Scanning from distance (title, figures)
+- **2-4 minutes**: Reading key points up close
+- **5+ minutes**: Engaged conversation (if interested)
+
+**Design Implication**: Poster must work at three levels:
+1. **Distance view** (6-10 feet): Title and main figure visible
+2. **Browse view** (3-6 feet): Section headers and key results readable
+3. **Detail view** (1-3 feet): Full content accessible
+
+### 2. Tell a Story, Not a Paper
+
+**Poster ≠ Condensed Paper**
+
+**Paper approach** (❌):
+- Comprehensive literature review
+- Detailed methodology
+- All results presented
+- Lengthy discussion
+- 50+ references
+
+**Poster approach** (✅):
+- One sentence background
+- Visual methods diagram
+- 3-5 key results
+- 3-4 bullet point conclusions
+- 5-10 key references
+
+**Story Arc for Posters**:
+```
+Hook (Problem) → Approach → Discovery → Impact
+```
+
+**Example**:
+- **Hook**: "Antibiotic resistance threatens millions of lives annually"
+- **Approach**: "We developed an AI system to predict resistance patterns"
+- **Discovery**: "Our model achieves 87% accuracy, 20% better than existing methods"
+- **Impact**: "Could reduce treatment failures by identifying resistance earlier"
+
+### 3. The 800-Word Maximum
+
+**Word Count Guidelines**:
+- **Ideal**: 300-500 words
+- **Maximum**: 800 words
+- **Hard limit**: 1000 words (beyond this, poster is unreadable)
+
+**Word Budget by Section**:
+| Section | Word Count | % of Total |
+|---------|-----------|------------|
+| Introduction/Background | 50-100 | 15% |
+| Methods | 100-150 | 25% |
+| Results (text) | 100-200 | 25% |
+| Discussion/Conclusions | 100-150 | 25% |
+| References/Acknowledgments | 50-100 | 10% |
+
+**Counting Tool**:
+```latex
+% Add word count to poster (remove for final)
+\usepackage{texcount}
+% Compile with: texcount -inc poster.tex
+```
+
+### 4. Visual-to-Text Ratio
+
+**Optimal Balance**: 40-50% visual content, 50-60% text+white space
+
+**Visual Content Includes**:
+- Figures and graphs
+- Photos and images
+- Diagrams and flowcharts
+- Icons and symbols
+- Color blocks and design elements
+
+**Too Text-Heavy** (❌):
+- Wall of text
+- Small figures
+- Intimidating to viewers
+- Low engagement
+
+**Well-Balanced** (✅):
+- Clear figures dominate
+- Text supports visuals
+- Easy to scan
+- Inviting appearance
+
+## Section-Specific Content Guidance
+
+### Title
+
+**Purpose**: Capture attention, convey topic, establish credibility
+
+**Characteristics of Effective Titles**:
+- **Concise**: 10-15 words maximum
+- **Descriptive**: Clearly states research topic
+- **Active**: Uses strong verbs when possible
+- **Specific**: Avoids vague terms
+- **Jargon-aware**: Balances field-specific terms with accessibility
+
+**Title Formulas**:
+
+**1. Descriptive**:
+```
+[Method/Approach] for [Problem/Application]
+
+Example: "Deep Learning for Early Detection of Alzheimer's Disease"
+```
+
+**2. Question**:
+```
+[Research Question]?
+
+Example: "Can Microbiome Diversity Predict Treatment Response?"
+```
+
+**3. Assertion**:
+```
+[Finding] in [Context]
+
+Example: "Novel Mechanism Identified in Drug Resistance Pathways"
+```
+
+**4. Colon Format**:
+```
+[Topic]: [Specific Approach/Finding]
+
+Example: "Urban Heat Islands: A Machine Learning Framework for Mitigation"
+```
+
+**Avoid**:
+- ❌ Generic titles: "A Study of X"
+- ❌ Overly cute or clever wordplay (confuses message)
+- ❌ Excessive jargon: "Utilization of CRISPR-Cas9..."
+- ❌ Unnecessarily long: "Investigation of the potential role of..."
+
+**LaTeX Title Formatting**:
+```latex
+% Emphasize key words with bold
+\title{Deep Learning for \textbf{Early Detection} of Alzheimer's Disease}
+
+% Two-line titles for long names
+\title{Machine Learning Framework for\\Urban Heat Island Mitigation}
+
+% Avoid ALL CAPS (harder to read)
+```
+
+### Authors and Affiliations
+
+**Best Practices**:
+- **Presenting author**: Bold, underline, or asterisk
+- **Corresponding author**: Include email
+- **Affiliations**: Superscript numbers or symbols
+- **Institutional logos**: 2-4 maximum
+
+**Format Examples**:
+```latex
+% Simple format
+\author{\textbf{Jane Smith}\textsuperscript{1}, John Doe\textsuperscript{2}}
+\institute{
+ \textsuperscript{1}University of Example,
+ \textsuperscript{2}Research Institute
+}
+
+% With contact
+\author{Jane Smith\textsuperscript{1,*}}
+\institute{
+ \textsuperscript{1}Department, University\\
+ \textsuperscript{*}jane.smith@university.edu
+}
+```
+
+### Introduction/Background
+
+**Purpose**: Establish context, motivate research, state objective
+
+**Structure** (50-100 words):
+1. **Problem statement** (1-2 sentences): What's the issue?
+2. **Knowledge gap** (1-2 sentences): What's unknown/unsolved?
+3. **Research objective** (1 sentence): What did you do?
+
+**Example** (95 words):
+```
+Antibiotic resistance causes 700,000 deaths annually, projected to reach
+10 million by 2050. Current diagnostic methods require 48-72 hours,
+delaying appropriate treatment. Machine learning offers potential for
+rapid resistance prediction, but existing models lack generalizability
+across bacterial species.
+
+We developed a transformer-based deep learning model to predict antibiotic
+resistance from genomic sequences across multiple pathogen species. Our
+approach integrates evolutionary information and protein structure to
+improve cross-species accuracy.
+```
+
+**Visual Support**:
+- Conceptual diagram showing problem
+- Infographic with statistics
+- Image of application context
+
+**Common Mistakes**:
+- ❌ Extensive literature review
+- ❌ Too much background detail
+- ❌ Undefined acronyms at first use
+- ❌ Missing clear objective statement
+
+### Methods
+
+**Purpose**: Describe approach sufficiently for understanding (not replication)
+
+**Key Question**: "How did you do it?" not "How could someone else replicate it?"
+
+**Content Strategy**:
+- **Prioritize**: Visual methods diagram > text description
+- **Include**: Study design, key procedures, analysis approach
+- **Omit**: Detailed protocols, routine procedures, specific reagent details
+
+**Visual Methods (Highly Recommended)**:
+```latex
+% Flowchart of study design
+\begin{tikzpicture}[node distance=2cm]
+ \node (start) [box] {Data Collection\\n=1,000 samples};
+ \node (process) [box, below of=start] {Preprocessing\\Quality Control};
+ \node (analysis) [box, below of=process] {Statistical Analysis\\Mixed Models};
+ \node (end) [box, below of=analysis] {Validation\\Independent Cohort};
+
+ \draw [arrow] (start) -- (process);
+ \draw [arrow] (process) -- (analysis);
+ \draw [arrow] (analysis) -- (end);
+\end{tikzpicture}
+```
+
+**Text Methods** (50-150 words):
+
+**For Experimental Studies**:
+```
+Methods
+• Study design: Randomized controlled trial (n=200)
+• Participants: Adults aged 18-65 with Type 2 diabetes
+• Intervention: 12-week exercise program vs. standard care
+• Outcomes: HbA1c (primary), insulin sensitivity (secondary)
+• Analysis: Linear mixed models, intention-to-treat
+```
+
+**For Computational Studies**:
+```
+Methods
+• Dataset: 10,000 labeled images from ImageNet
+• Architecture: ResNet-50 with custom attention mechanism
+• Training: 100 epochs, Adam optimizer, learning rate 0.001
+• Validation: 5-fold cross-validation
+• Comparison: Baseline CNN, VGG-16, Inception-v3
+```
+
+**Format Options**:
+- **Bullet points**: Quick scanning (recommended)
+- **Numbered list**: Sequential procedures
+- **Diagram + brief text**: Ideal combination
+- **Table**: Multiple conditions or parameters
+
+### Results
+
+**Purpose**: Present key findings visually and clearly
+
+**Golden Rule**: Show, don't tell
+
+**Content Allocation**:
+- **Figures**: 70-80% of Results section
+- **Text**: 20-30% (brief descriptions, statistics)
+
+**How Many Results**:
+- **Ideal**: 3-5 main findings
+- **Maximum**: 6-7 distinct results
+- **Focus**: Primary outcomes, most impactful findings
+
+**Figure Selection Criteria**:
+1. Does it support the main message?
+2. Is it self-explanatory with caption?
+3. Can it be understood in 10 seconds?
+4. Does it add information beyond text?
+
+**Figure Captions**:
+- **Descriptive**: Explain what is shown
+- **Standalone**: Understandable without reading full poster
+- **Statistical**: Include significance indicators, sample sizes
+- **Concise**: 1-3 sentences
+
+**Example Caption**:
+```latex
+\caption{Treatment significantly improved outcomes.
+Mean±SD shown for control (blue, n=45) and treatment (orange, n=47) groups.
+**p<0.01, ***p<0.001 (two-tailed t-test).}
+```
+
+**Text Support for Results** (100-200 words):
+- State main finding per figure
+- Include key statistics
+- Note trends or patterns
+- Avoid detailed interpretation (save for Discussion)
+
+**Example Results Text**:
+```
+Key Findings
+• Model achieved 87% accuracy on test set (vs. 73% baseline)
+• Performance consistent across 5 bacterial species (p<0.001)
+• Prediction speed: <30 seconds per isolate
+• Feature importance: protein structure (42%), sequence (35%),
+ evolutionary conservation (23%)
+```
+
+**Data Presentation Formats**:
+
+**1. Bar Charts**: Comparing categories
+```latex
+\begin{tikzpicture}
+ \begin{axis}[
+ ybar,
+ ylabel=Accuracy (\%),
+ symbolic x coords={Baseline, Model A, Our Method},
+ xtick=data,
+ nodes near coords
+ ]
+ \addplot coordinates {(Baseline,73) (Model A,81) (Our Method,87)};
+ \end{axis}
+\end{tikzpicture}
+```
+
+**2. Line Graphs**: Trends over time
+**3. Scatter Plots**: Correlations
+**4. Heatmaps**: Matrix data, clustering
+**5. Box Plots**: Distributions, comparisons
+**6. ROC Curves**: Classification performance
+
+### Discussion/Conclusions
+
+**Purpose**: Interpret findings, state implications, acknowledge limitations
+
+**Structure** (100-150 words):
+
+**1. Main Conclusions** (50-75 words):
+- 3-5 bullet points
+- Clear, specific takeaways
+- Linked to research objectives
+
+**Example**:
+```
+Conclusions
+• First cross-species model for antibiotic resistance prediction
+ achieving >85% accuracy
+• Protein structure integration critical for generalizability
+ (improved accuracy by 14%)
+• Prediction speed enables clinical decision support within
+ consultation timeframe
+• Potential to reduce inappropriate antibiotic use by 20-30%
+```
+
+**2. Limitations** (25-50 words, optional but recommended):
+- Acknowledge key constraints
+- Brief, honest
+- Shows scientific rigor
+
+**Example**:
+```
+Limitations
+• Training data limited to 5 bacterial species
+• Requires genomic sequencing (not widely available)
+• Validation needed in prospective clinical trials
+```
+
+**3. Future Directions** (25-50 words, optional):
+- Next steps
+- Broader implications
+- Call to action
+
+**Example**:
+```
+Next Steps
+• Expand to 20+ additional species
+• Develop point-of-care sequencing integration
+• Launch multi-center clinical validation study (2025)
+```
+
+**Avoid**:
+- ❌ Overstating findings: "This revolutionary breakthrough..."
+- ❌ Extensive comparison to other work
+- ❌ New results in Discussion
+- ❌ Vague conclusions: "Further research is needed"
+
+### References
+
+**How Many**: 5-10 key citations
+
+**Selection Criteria**:
+- Include seminal work in the field
+- Recent relevant studies (last 5 years)
+- Methods cited in your poster
+- Controversial claims that need support
+
+**Format**: Abbreviated, consistent style
+
+**Examples**:
+
+**Numbered (Vancouver)**:
+```
+References
+1. Smith et al. (2023). Nature. 615:234-240.
+2. Jones & Lee (2024). Science. 383:112-118.
+3. Chen et al. (2022). Cell. 185:456-470.
+```
+
+**Author-Year (APA)**:
+```
+References
+Smith, J. et al. (2023). Title. Nature, 615, 234-240.
+Jones, A., & Lee, B. (2024). Title. Science, 383, 112-118.
+```
+
+**Minimal (For Space Constraints)**:
+```
+Key References: Smith (Nature 2023), Jones (Science 2024),
+Chen (Cell 2022). Full bibliography: [QR Code]
+```
+
+**Alternative**: QR code linking to full reference list
+
+### Acknowledgments
+
+**Include**:
+- Funding sources (with grant numbers)
+- Major collaborators
+- Core facilities used
+- Dataset sources
+
+**Format** (25-50 words):
+```
+Acknowledgments
+Funded by NIH Grant R01-123456 and NSF Award 7890123.
+We thank Dr. X for data access, the Y Core Facility for
+sequencing, and Z for helpful discussions.
+```
+
+### Contact Information
+
+**Essential Elements**:
+- Name of presenting/corresponding author
+- Email address
+- Optional: Lab website, Twitter/X, LinkedIn, ORCID
+
+**Format**:
+```
+Contact: Jane Smith, jane.smith@university.edu
+Lab: smithlab.university.edu | Twitter: @smithlab
+```
+
+**QR Code Alternative**:
+- Link to personal/lab website
+- Link to paper preprint/publication
+- Link to code repository (GitHub)
+- Link to supplementary materials
+
+## Writing Style for Posters
+
+### Active vs. Passive Voice
+
+**Prefer Active Voice** (more engaging, clearer):
+- ✅ "We developed a model..."
+- ✅ "The treatment reduced symptoms..."
+
+**Passive Voice** (when appropriate):
+- ✅ "Samples were collected from..."
+- ✅ "Data were analyzed using..."
+
+### Sentence Length
+
+**Keep Sentences Short**:
+- **Ideal**: 10-15 words per sentence
+- **Maximum**: 20-25 words
+- **Avoid**: >30 words (hard to follow)
+
+**Example Revision**:
+- ❌ Long: "We performed a comprehensive analysis of gene expression data from 500 patients with colorectal cancer using RNA sequencing and identified 47 differentially expressed genes associated with treatment response." (31 words)
+- ✅ Short: "We analyzed RNA sequencing data from 500 colorectal cancer patients. We identified 47 genes associated with treatment response." (19 words total, two sentences)
+
+### Bullet Points vs. Paragraphs
+
+**Use Bullet Points For**:
+- ✅ Lists of items or findings
+- ✅ Key conclusions
+- ✅ Methods steps
+- ✅ Study characteristics
+
+**Use Short Paragraphs For**:
+- ✅ Narrative flow (Introduction)
+- ✅ Complex explanations
+- ✅ Connected ideas
+
+**Bullet Point Best Practices**:
+- Start with action verbs or nouns
+- Parallel structure throughout list
+- 3-7 bullets per list (not too many)
+- Brief (1-2 lines each)
+
+**Example**:
+```
+Methods
+• Participants: 200 adults (18-65 years)
+• Design: Double-blind RCT (12 weeks)
+• Intervention: Daily 30-min exercise
+• Control: Standard care
+• Analysis: Mixed models (SPSS v.28)
+```
+
+### Acronyms and Jargon
+
+**First Use Rule**: Define at first appearance
+```
+We used machine learning (ML) to analyze... Later, ML predicted...
+```
+
+**Common Acronyms**: May not need definition if universal to field
+- DNA, RNA, MRI, CT, PCR (in biomedical context)
+- AI, ML, CNN (in computer science context)
+
+**Avoid Excessive Jargon**:
+- ❌ "Utilized" → ✅ "Used"
+- ❌ "Implement utilization of" → ✅ "Use"
+- ❌ "A majority of" → ✅ "Most"
+
+### Numbers and Statistics
+
+**Present Statistics Clearly**:
+- Always include measure of variability (SD, SE, CI)
+- Report sample sizes: n=50
+- Indicate significance: p<0.05, p<0.01, p<0.001
+- Use symbols consistently: * for p<0.05, ** for p<0.01
+
+**Format Numbers**:
+- Round appropriately (avoid false precision)
+- Use consistent decimal places
+- Include units: 25 mg/dL, 37°C
+- Large numbers: 1,000 or 1000 (be consistent)
+
+**Example**:
+```
+Treatment increased response by 23.5% (95% CI: 18.2-28.8%, p<0.001, n=150)
+```
+
+## Visual-Text Integration
+
+### Figure-Text Relationship
+
+**Figure First, Text Second**:
+1. Design poster around key figures
+2. Add text to support and explain visuals
+3. Ensure figures can stand alone
+
+**Text Placement Relative to Figures**:
+- **Above**: Context, "What you're about to see"
+- **Below**: Explanation, statistics, caption
+- **Beside**: Comparison, interpretation
+
+### Callouts and Annotations
+
+**On-Figure Annotations**:
+```latex
+\begin{tikzpicture}
+ \node[inner sep=0] (img) {\includegraphics[width=10cm]{figure.pdf}};
+ \draw[->, thick, red] (8,5) -- (6,3) node[left] {Key region};
+ \draw[red, thick] (3,2) circle (1cm) node[above=1.2cm] {Anomaly};
+\end{tikzpicture}
+```
+
+**Callout Boxes**:
+```latex
+\begin{tcolorbox}[colback=yellow!10, colframe=orange!80,
+ title=Key Finding]
+Our method reduces errors by 34\% compared to state-of-the-art.
+\end{tcolorbox}
+```
+
+### Icons for Section Headers
+
+**Visual Section Markers**:
+```latex
+\usepackage{fontawesome5}
+
+\block{\faFlask~Introduction}{...}
+\block{\faCog~Methods}{...}
+\block{\faChartBar~Results}{...}
+\block{\faLightbulb~Conclusions}{...}
+```
+
+## Content Adaptation Strategies
+
+### From Paper to Poster
+
+**Condensation Process**:
+
+**1. Identify Core Message** (The Elevator Pitch):
+- What's the one thing you want people to remember?
+- If you had 30 seconds, what would you say?
+
+**2. Select Key Results**:
+- Choose 3-5 most impactful findings
+- Omit supporting/secondary results
+- Focus on figures with strong visual impact
+
+**3. Simplify Methods**:
+- Visual flowchart > text description
+- Omit routine procedures
+- Include only essential parameters
+
+**4. Trim Literature Review**:
+- One sentence background
+- One sentence gap/motivation
+- One sentence your contribution
+
+**5. Condense Discussion**:
+- Main conclusions only
+- Brief limitations
+- One sentence future direction
+
+### For Different Audiences
+
+**Specialist Audience** (Same Field):
+- Can use field-specific jargon
+- Less background needed
+- Focus on novel methodology
+- Emphasize nuanced findings
+
+**General Scientific Audience**:
+- Define key terms
+- More context/background
+- Broader implications
+- Visual metaphors helpful
+
+**Public/Lay Audience**:
+- Minimal jargon, all defined
+- Extensive context
+- Real-world applications
+- Analogies and simple language
+
+**Example Adaptation**:
+
+**Specialist**: "CRISPR-Cas9 knockout of BRCA1 induced synthetic lethality with PARP inhibitors"
+
+**General**: "We used gene editing to make cancer cells vulnerable to existing drugs"
+
+**Public**: "We found a way to make cancer treatments work better by targeting specific genetic weaknesses"
+
+## Quality Control Checklist
+
+### Content Review
+
+**Clarity**:
+- [ ] Main message immediately clear
+- [ ] All acronyms defined
+- [ ] Sentences short and direct
+- [ ] No unnecessary jargon
+
+**Completeness**:
+- [ ] Research question/objective stated
+- [ ] Methods sufficiently described
+- [ ] Key results presented
+- [ ] Conclusions drawn
+- [ ] Limitations acknowledged
+
+**Accuracy**:
+- [ ] All statistics correct
+- [ ] Figure captions accurate
+- [ ] References properly cited
+- [ ] No overstated claims
+
+**Engagement**:
+- [ ] Compelling title
+- [ ] Visual interest
+- [ ] Clear take-home message
+- [ ] Conversation starters
+
+### Readability Testing
+
+**Distance Test**:
+- Print at 25% scale
+- View from 2-3 feet (simulates 8-12 feet for full poster)
+- Can you read: Title? Section headers? Body text?
+
+**Scan Test**:
+- Give poster to colleague for 30 seconds
+- Ask: "What is this poster about?"
+- They should identify: Topic, approach, main finding
+
+**Detail Test**:
+- Ask colleague to read poster thoroughly (5 min)
+- Ask: "What are the key conclusions?"
+- Verify understanding matches your intent
+
+## Common Content Mistakes
+
+**1. Too Much Text**
+- ❌ >1000 words
+- ❌ Long paragraphs
+- ❌ Full paper condensed
+- ✅ 300-800 words, bullet points, key findings only
+
+**2. Unclear Message**
+- ❌ Multiple unrelated findings
+- ❌ No clear conclusion
+- ❌ Vague implications
+- ✅ 1-3 main points, explicit conclusions
+
+**3. Methods Overkill**
+- ❌ Detailed protocols
+- ❌ All parameters listed
+- ❌ Routine procedures described
+- ✅ Visual flowchart, key details only
+
+**4. Poor Figure Integration**
+- ❌ Figures without context
+- ❌ Unclear captions
+- ❌ Text doesn't reference figures
+- ✅ Figures central, well-captioned, text integrated
+
+**5. Missing Context**
+- ❌ No background
+- ❌ Undefined acronyms
+- ❌ Assumes expert knowledge
+- ✅ Brief context, definitions, accessible to broader audience
+
+## Conclusion
+
+Effective poster content:
+- **Concise**: 300-800 words maximum
+- **Visual**: 40-50% figures and graphics
+- **Clear**: One main message, 3-5 key findings
+- **Engaging**: Compelling story, not just facts
+- **Accessible**: Appropriate for target audience
+- **Actionable**: Clear implications and next steps
+
+Remember: Your poster is a conversation starter, not a comprehensive treatise. Design content to intrigue, engage, and invite discussion.
+
diff --git a/scientific-skills/latex-posters/references/poster_design_principles.md b/scientific-skills/latex-posters/references/poster_design_principles.md
new file mode 100644
index 0000000..2454bff
--- /dev/null
+++ b/scientific-skills/latex-posters/references/poster_design_principles.md
@@ -0,0 +1,806 @@
+# Research Poster Design Principles
+
+## Overview
+
+Effective poster design balances visual appeal, readability, and scientific content. This guide covers typography, color theory, visual hierarchy, accessibility, and evidence-based design principles for research posters.
+
+## Core Design Principles
+
+### 1. Visual Hierarchy
+
+Guide viewers through content in logical order using size, color, position, and contrast.
+
+**Hierarchy Levels**:
+
+1. **Primary (Title)**: Largest, most prominent
+ - Size: 72-120pt
+ - Position: Top center or top spanning
+ - Weight: Bold
+ - Purpose: Capture attention from 20+ feet
+
+2. **Secondary (Section Headers)**: Organize content
+ - Size: 48-72pt
+ - Weight: Bold or semi-bold
+ - Purpose: Section navigation, readable from 10 feet
+
+3. **Tertiary (Body Text)**: Main content
+ - Size: 24-36pt minimum
+ - Weight: Regular
+ - Purpose: Detailed information, readable from 4-6 feet
+
+4. **Quaternary (Captions, References)**: Supporting info
+ - Size: 18-24pt
+ - Weight: Regular or light
+ - Purpose: Context and attribution
+
+**Implementation**:
+```latex
+% Define hierarchy in LaTeX
+\setbeamerfont{title}{size=\VeryHuge,series=\bfseries} % 90pt+
+\setbeamerfont{block title}{size=\Huge,series=\bfseries} % 60pt
+\setbeamerfont{block body}{size=\LARGE} % 30pt
+\setbeamerfont{caption}{size=\large} % 24pt
+```
+
+### 2. White Space (Negative Space)
+
+Empty space is not wasted space—it enhances readability and guides attention.
+
+**White Space Functions**:
+- **Breathing room**: Prevents overwhelming viewers
+- **Grouping**: Shows which elements belong together
+- **Focus**: Draws attention to important elements
+- **Flow**: Creates visual pathways through content
+
+**Guidelines**:
+- Minimum 5-10% margins on all sides
+- Consistent spacing between blocks (1-2cm)
+- Space around figures equal to or greater than border width
+- Group related items closely, separate unrelated items
+- Don't fill every inch—aim for 40-60% text coverage
+
+**LaTeX Implementation**:
+```latex
+% beamerposter spacing
+\setbeamertemplate{block begin}{
+ \vskip2ex % Space before block
+ ...
+}
+
+% tikzposter spacing
+\documentclass[..., blockverticalspace=15mm, colspace=15mm]{tikzposter}
+
+% Manual spacing
+\vspace{2cm} % Vertical space
+\hspace{1cm} % Horizontal space
+```
+
+### 3. Alignment and Grid Systems
+
+Proper alignment creates professional, organized appearance.
+
+**Alignment Types**:
+- **Left-aligned text**: Most readable for body text (Western audiences)
+- **Center-aligned**: Headers, titles, symmetric layouts
+- **Right-aligned**: Rarely used, special cases only
+- **Justified**: Avoid (creates uneven spacing)
+
+**Grid Systems**:
+- **2-column**: Simple, traditional, good for narrative flow
+- **3-column**: Most common, balanced, versatile
+- **4-column**: Complex, information-dense, requires careful design
+- **Asymmetric**: Creative, modern, requires expertise
+
+**Best Practices**:
+- Align block edges to invisible grid lines
+- Keep consistent column widths (unless intentionally asymmetric)
+- Align similar elements (all figures, all text blocks)
+- Use consistent margins throughout
+
+### 4. Visual Flow and Reading Patterns
+
+Design for natural eye movement and logical content progression.
+
+**Common Reading Patterns**:
+
+**Z-Pattern (Landscape posters)**:
+```
+Start → → → Top Right
+ ↓
+Middle Left → → Middle
+ ↓
+Bottom Left → → → End
+```
+
+**F-Pattern (Portrait posters)**:
+```
+Title → → → →
+↓
+Section 1 → →
+↓
+Section 2 → →
+↓
+Section 3 → →
+↓
+Conclusion → →
+```
+
+**Gutenberg Diagram**:
+```
+Primary Area Strong Fallow
+(top-left) (top-right)
+ ↓ ↓
+Weak Fallow Terminal Area
+(bottom-left) (bottom-right)
+```
+
+**Implementation Strategy**:
+1. Place most important content in "hot zones" (top-left, center)
+2. Create visual paths with arrows, lines, or color
+3. Use numbering for sequential information (Methods steps)
+4. Design left-to-right, top-to-bottom flow (Western audiences)
+5. Position conclusions prominently (bottom-right is natural endpoint)
+
+## Typography
+
+### Font Selection
+
+**Recommended Fonts**:
+
+**Sans-Serif (Recommended for posters)**:
+- **Helvetica**: Clean, professional, widely available
+- **Arial**: Similar to Helvetica, universal compatibility
+- **Calibri**: Modern, friendly, good readability
+- **Open Sans**: Contemporary, excellent web and print
+- **Roboto**: Modern, Google design, highly readable
+- **Lato**: Warm, professional, works at all sizes
+
+**Serif (Use sparingly)**:
+- **Times New Roman**: Traditional, formal
+- **Garamond**: Elegant, good for humanities
+- **Georgia**: Designed for screens, readable
+
+**Avoid**:
+- ❌ Comic Sans (unprofessional)
+- ❌ Decorative or script fonts (illegible from distance)
+- ❌ Mixing more than 2-3 font families
+
+**LaTeX Implementation**:
+```latex
+% Helvetica (sans-serif)
+\usepackage{helvet}
+\renewcommand{\familydefault}{\sfdefault}
+
+% Arial-like
+\usepackage{avant}
+\renewcommand{\familydefault}{\sfdefault}
+
+% Modern fonts with fontspec (requires LuaLaTeX/XeLaTeX)
+\usepackage{fontspec}
+\setmainfont{Helvetica Neue}
+\setsansfont{Open Sans}
+```
+
+### Font Sizing
+
+**Absolute Minimum Sizes** (readable from 4-6 feet):
+- Title: 72pt+ (85-120pt recommended)
+- Section headers: 48-72pt
+- Body text: 24-36pt (30pt+ recommended)
+- Captions/small text: 18-24pt
+- References: 16-20pt minimum
+
+**Testing Readability**:
+- Print at 25% scale
+- Read from 2-3 feet distance
+- If legible, full-scale poster will be readable from 8-12 feet
+
+**Size Conversion**:
+| LaTeX Command | Approximate Size | Use Case |
+|---------------|------------------|----------|
+| `\tiny` | 10pt | Avoid on posters |
+| `\small` | 16pt | Minimal use only |
+| `\normalsize` | 20pt | References (scaled up) |
+| `\large` | 24pt | Captions, small text |
+| `\Large` | 28pt | Body text (minimum) |
+| `\LARGE` | 32pt | Body text (recommended) |
+| `\huge` | 36pt | Subheadings |
+| `\Huge` | 48pt | Section headers |
+| `\VeryHuge` | 72pt+ | Title |
+
+### Text Formatting Best Practices
+
+**Use**:
+- ✅ **Bold** for emphasis and headers
+- ✅ Short paragraphs (3-5 lines maximum)
+- ✅ Bullet points for lists
+- ✅ Adequate line spacing (1.2-1.5)
+- ✅ High contrast (dark text on light background)
+
+**Avoid**:
+- ❌ Italics from distance (hard to read)
+- ❌ ALL CAPS FOR LONG TEXT (SLOW TO READ)
+- ❌ Underlines (old-fashioned, interferes with descenders)
+- ❌ Long paragraphs (> 6 lines)
+- ❌ Light text on light backgrounds
+
+**Line Spacing**:
+```latex
+% Increase line spacing for readability
+\usepackage{setspace}
+\setstretch{1.3} % 1.3x normal spacing
+
+% Or in specific blocks
+\begin{spacing}{1.5}
+ Your text here with extra spacing
+\end{spacing}
+```
+
+## Color Theory for Posters
+
+### Color Psychology and Meaning
+
+Colors convey meaning and affect viewer perception:
+
+| Color | Associations | Use Cases |
+|-------|--------------|-----------|
+| **Blue** | Trust, professionalism, science | Academic, medical, technology |
+| **Green** | Nature, health, growth | Environmental, biology, health |
+| **Red** | Energy, urgency, passion | Attention, warnings, bold statements |
+| **Orange** | Creativity, enthusiasm | Innovative research, friendly approach |
+| **Purple** | Wisdom, creativity, luxury | Humanities, arts, premium research |
+| **Gray** | Neutral, professional, modern | Technology, minimal designs |
+| **Yellow** | Optimism, attention, caution | Highlights, energy, caution areas |
+
+### Color Scheme Types
+
+**1. Monochromatic**: Variations of single hue
+- **Pros**: Harmonious, professional, easy to execute
+- **Cons**: Can be boring, less visual interest
+- **Use**: Conservative conferences, institutional branding
+
+```latex
+% Monochromatic blue scheme
+\definecolor{darkblue}{RGB}{0,51,102}
+\definecolor{medblue}{RGB}{51,102,153}
+\definecolor{lightblue}{RGB}{204,229,255}
+```
+
+**2. Analogous**: Adjacent colors on color wheel
+- **Pros**: Harmonious, visually comfortable
+- **Cons**: Low contrast, may lack excitement
+- **Use**: Nature/biology topics, smooth gradients
+
+```latex
+% Analogous blue-green scheme
+\definecolor{blue}{RGB}{0,102,204}
+\definecolor{teal}{RGB}{0,153,153}
+\definecolor{green}{RGB}{51,153,102}
+```
+
+**3. Complementary**: Opposite colors on wheel
+- **Pros**: High contrast, vibrant, energetic
+- **Cons**: Can be overwhelming if intense
+- **Use**: Drawing attention, modern designs
+
+```latex
+% Complementary blue-orange scheme
+\definecolor{primary}{RGB}{0,71,171} % Blue
+\definecolor{accent}{RGB}{255,127,0} % Orange
+```
+
+**4. Triadic**: Three evenly spaced colors
+- **Pros**: Balanced, vibrant, visually rich
+- **Cons**: Can appear busy if not balanced
+- **Use**: Multi-topic posters, creative fields
+
+```latex
+% Triadic scheme
+\definecolor{blue}{RGB}{0,102,204}
+\definecolor{red}{RGB}{204,0,51}
+\definecolor{yellow}{RGB}{255,204,0}
+```
+
+**5. Split-Complementary**: Base + two adjacent to complement
+- **Pros**: High contrast but less tense than complementary
+- **Cons**: Complex to balance
+- **Use**: Sophisticated designs, experienced designers
+
+### High-Contrast Combinations
+
+Ensure readability with sufficient contrast:
+
+**Excellent Contrast (Use these)**:
+- Dark blue on white
+- Black on white
+- White on dark blue/green/purple
+- Dark gray on light yellow
+- Black on light cyan
+
+**Poor Contrast (Avoid)**:
+- ❌ Red on green (color-blind issue)
+- ❌ Yellow on white
+- ❌ Light gray on white
+- ❌ Blue on black (hard to read)
+- ❌ Any pure colors on each other
+
+**Contrast Ratio Standards**:
+- Minimum: 4.5:1 (WCAG AA)
+- Recommended: 7:1 (WCAG AAA)
+- Test at: https://webaim.org/resources/contrastchecker/
+
+**LaTeX Color Contrast**:
+```latex
+% High contrast header
+\setbeamercolor{block title}{bg=black, fg=white}
+
+% Medium contrast body
+\setbeamercolor{block body}{bg=gray!10, fg=black}
+
+% Check contrast manually or use online tools
+```
+
+### Color-Blind Friendly Palettes
+
+~8% of males and ~0.5% of females have color vision deficiency.
+
+**Safe Color Combinations**:
+- Blue + Orange (most universally distinguishable)
+- Blue + Yellow
+- Blue + Red
+- Purple + Green (use with caution)
+
+**Avoid**:
+- ❌ Red + Green (indistinguishable to most common color blindness)
+- ❌ Green + Brown
+- ❌ Blue + Purple (can be problematic)
+- ❌ Light green + Yellow
+
+**Recommended Palettes**:
+
+**IBM Color Blind Safe** (excellent accessibility):
+```latex
+\definecolor{ibmblue}{RGB}{100,143,255}
+\definecolor{ibmmagenta}{RGB}{254,97,0}
+\definecolor{ibmpurple}{RGB}{220,38,127}
+\definecolor{ibmcyan}{RGB}{33,191,115}
+```
+
+**Okabe-Ito Palette** (scientifically tested):
+```latex
+\definecolor{okorange}{RGB}{230,159,0}
+\definecolor{okskyblue}{RGB}{86,180,233}
+\definecolor{okgreen}{RGB}{0,158,115}
+\definecolor{okyellow}{RGB}{240,228,66}
+\definecolor{okblue}{RGB}{0,114,178}
+\definecolor{okvermillion}{RGB}{213,94,0}
+\definecolor{okpurple}{RGB}{204,121,167}
+```
+
+**Paul Tol's Bright Palette**:
+```latex
+\definecolor{tolblue}{RGB}{68,119,170}
+\definecolor{tolred}{RGB}{204,102,119}
+\definecolor{tolgreen}{RGB}{34,136,51}
+\definecolor{tolyellow}{RGB}{238,221,136}
+\definecolor{tolcyan}{RGB}{102,204,238}
+```
+
+### Institutional Branding
+
+Match university or department colors:
+
+```latex
+% Example: Stanford colors
+\definecolor{stanford-red}{RGB}{140,21,21}
+\definecolor{stanford-gray}{RGB}{83,86,90}
+
+% Example: MIT colors
+\definecolor{mit-red}{RGB}{163,31,52}
+\definecolor{mit-gray}{RGB}{138,139,140}
+
+% Example: Cambridge colors
+\definecolor{cambridge-blue}{RGB}{163,193,173}
+\definecolor{cambridge-lblue}{RGB}{212,239,223}
+```
+
+## Accessibility Considerations
+
+### Universal Design Principles
+
+Design posters usable by the widest range of people:
+
+**1. Visual Accessibility**:
+- High contrast text (minimum 4.5:1 ratio)
+- Large font sizes (24pt+ body text)
+- Color-blind safe palettes
+- Clear visual hierarchy
+- Avoid relying solely on color to convey information
+
+**2. Cognitive Accessibility**:
+- Clear, simple language
+- Logical organization
+- Consistent layout
+- Visual cues for navigation (arrows, numbers)
+- Avoid clutter and information overload
+
+**3. Physical Accessibility**:
+- Position critical content at wheelchair-accessible height (3-5 feet)
+- Include QR codes to digital versions
+- Provide printed handouts for detail viewing
+- Consider lighting and reflection in poster material choice
+
+### Alternative Text and Descriptions
+
+Make posters accessible to screen readers (for digital versions):
+
+```latex
+% Add alt text to figures
+\includegraphics[width=\linewidth]{figure.pdf}
+% Alternative: Include detailed caption
+\caption{Bar graph showing mean±SD of treatment outcomes.
+Control group (blue): 45±5\%; Treatment group (orange): 78±6\%.
+Asterisks indicate significance: *p<0.05, **p<0.01.}
+```
+
+### Multi-Modal Information
+
+Don't rely on single sensory channel:
+
+**Use Redundant Encoding**:
+- Color + Shape (not just color for categories)
+- Color + Pattern (hatching, stippling)
+- Color + Label (text labels on graph elements)
+- Text + Icons (visual + verbal)
+
+**Example**:
+```latex
+% Good: Color + shape + label
+\begin{tikzpicture}
+ \draw[fill=blue, circle] (0,0) circle (0.3) node[right] {Male: 45\%};
+ \draw[fill=red, rectangle] (0,-1) rectangle (0.6,-0.4) node[right] {Female: 55\%};
+\end{tikzpicture}
+```
+
+## Layout Composition
+
+### Rule of Thirds
+
+Divide poster into 3×3 grid; place key elements at intersections:
+
+```
++-----+-----+-----+
+| × | | × | ← Top third (title, logos)
++-----+-----+-----+
+| | × | | ← Middle third (main content)
++-----+-----+-----+
+| × | | × | ← Bottom third (conclusions)
++-----+-----+-----+
+ ↑ ↑
+Left Right
+```
+
+**Power Points** (intersections):
+- Top-left: Primary section start
+- Top-right: Logos, QR codes
+- Center: Key figure or main result
+- Bottom-right: Conclusions, contact
+
+### Balance and Symmetry
+
+**Symmetric Layouts**:
+- Formal, traditional, stable
+- Easy to design
+- Can appear static or boring
+- Good for conservative audiences
+
+**Asymmetric Layouts**:
+- Dynamic, modern, interesting
+- Harder to execute well
+- More visually engaging
+- Good for creative fields
+
+**Visual Weight Balance**:
+- Large elements = heavy weight
+- Dark colors = heavy weight
+- Dense text = heavy weight
+- Distribute weight evenly across poster
+
+### Proximity and Grouping
+
+**Gestalt Principles**:
+
+**Proximity**: Items close together are perceived as related
+```
+[Introduction] [Methods]
+
+[Results] [Discussion]
+```
+
+**Similarity**: Similar items are perceived as grouped
+- Use consistent colors for related sections
+- Same border styles for similar content types
+
+**Continuity**: Eyes follow lines and paths
+- Use arrows to guide through methods
+- Align elements to create invisible lines
+
+**Closure**: Mind completes incomplete shapes
+- Use partial borders to group without boxing in
+
+## Visual Elements
+
+### Icons and Graphics
+
+Strategic use of icons enhances comprehension:
+
+**Benefits**:
+- Universal language (crosses linguistic barriers)
+- Faster processing than text
+- Adds visual interest
+- Clarifies concepts
+
+**Best Practices**:
+- Use consistent style (all line, all filled, all flat)
+- Appropriate size (1-3cm typical)
+- Label ambiguous icons
+- Source: Font Awesome, Noun Project, academic icon sets
+
+**LaTeX Implementation**:
+```latex
+% Font Awesome icons
+\usepackage{fontawesome5}
+\faFlask{} Methods \quad \faChartBar{} Results
+
+% Custom icons with TikZ
+\begin{tikzpicture}
+ \node[circle, draw, thick, minimum size=1cm] {\Huge \faAtom};
+\end{tikzpicture}
+```
+
+### Borders and Dividers
+
+**Use Borders To**:
+- Define sections
+- Group related content
+- Add visual interest
+- Match institutional branding
+
+**Border Styles**:
+- Solid lines: Traditional, formal
+- Dashed lines: Informal, secondary info
+- Rounded corners: Friendly, modern
+- Drop shadows: Depth, modern (use sparingly)
+
+**Guidelines**:
+- Keep consistent width (2-5pt typical)
+- Use sparingly (not every element needs a border)
+- Match border color to content or theme
+- Ensure sufficient padding inside borders
+
+```latex
+% tikzposter borders
+\usecolorstyle{Denmark}
+\tikzposterlatexaffectionproofoff % Remove bottom-right logo
+
+% Custom border style
+\defineblockstyle{CustomBlock}{
+ titlewidthscale=1, bodywidthscale=1, titleleft,
+ titleoffsetx=0pt, titleoffsety=0pt, bodyoffsetx=0pt, bodyoffsety=0pt,
+ bodyverticalshift=0pt, roundedcorners=10, linewidth=2pt,
+ titleinnersep=8mm, bodyinnersep=8mm
+}{
+ \draw[draw=blocktitlebgcolor, fill=blockbodybgcolor,
+ rounded corners=\blockroundedcorners, line width=\blocklinewidth]
+ (blockbody.south west) rectangle (blocktitle.north east);
+}
+```
+
+### Background and Texture
+
+**Background Options**:
+
+**Plain (Recommended)**:
+- White or very light color
+- Maximum readability
+- Professional
+- Print-friendly
+
+**Gradient**:
+- Subtle gradients acceptable
+- Top-to-bottom or radial
+- Avoid strong contrasts that interfere with text
+
+**Textured**:
+- Very subtle textures only
+- Watermarks of logos/molecules (5-10% opacity)
+- Avoid patterns that create visual noise
+
+**Avoid**:
+- ❌ Busy backgrounds
+- ❌ Images behind text
+- ❌ High contrast backgrounds
+- ❌ Repeating patterns that cause visual artifacts
+
+```latex
+% Gradient background in tikzposter
+\documentclass{tikzposter}
+\definecolorstyle{GradientStyle}{
+ % ...color definitions...
+}{
+ \colorlet{backgroundcolor}{white!90!blue}
+ \colorlet{framecolor}{white!70!blue}
+}
+
+% Watermark
+\usepackage{tikz}
+\AddToShipoutPictureBG{
+ \AtPageCenter{
+ \includegraphics[width=0.5\paperwidth,opacity=0.05]{university-seal.pdf}
+ }
+}
+```
+
+## Common Design Mistakes
+
+### Critical Errors
+
+**1. Too Much Text** (Most common mistake)
+- ❌ More than 1000 words
+- ❌ Long paragraphs (>5 lines)
+- ❌ Small font sizes to fit more content
+- ✅ Solution: Cut ruthlessly, use bullet points, focus on key messages
+
+**2. Poor Contrast**
+- ❌ Light text on light background
+- ❌ Colored text on colored background
+- ✅ Solution: Dark on light or light on dark, test contrast ratio
+
+**3. Font Size Too Small**
+- ❌ Body text under 24pt
+- ❌ Trying to fit full paper content
+- ✅ Solution: 30pt+ body text, prioritize key findings
+
+**4. Cluttered Layout**
+- ❌ No white space
+- ❌ Elements touching edges
+- ❌ Random placement
+- ✅ Solution: Generous margins, grid alignment, intentional white space
+
+**5. Inconsistent Styling**
+- ❌ Multiple font families
+- ❌ Varying header styles
+- ❌ Misaligned elements
+- ✅ Solution: Define style guide, use templates, align to grid
+
+### Moderate Issues
+
+**6. Poor Figure Quality**
+- ❌ Pixelated images (<300 DPI)
+- ❌ Tiny axis labels
+- ❌ Unreadable legends
+- ✅ Solution: Vector graphics (PDF/SVG), large labels, clear legends
+
+**7. Color Overload**
+- ❌ Too many colors (>5 distinct hues)
+- ❌ Neon or overly saturated colors
+- ✅ Solution: Limit to 2-3 main colors, use tints/shades for variation
+
+**8. Ignoring Visual Hierarchy**
+- ❌ All text same size
+- ❌ No clear entry point
+- ✅ Solution: Vary sizes significantly, clear title, visual flow
+
+**9. Information Overload**
+- ❌ Trying to show everything
+- ❌ Too many figures
+- ✅ Solution: Show 3-5 key results, link to full paper via QR code
+
+**10. Poor Typography**
+- ❌ Justified text (uneven spacing)
+- ❌ All caps body text
+- ❌ Mixing serif and sans-serif randomly
+- ✅ Solution: Left-align body, sentence case, consistent fonts
+
+## Design Checklist
+
+### Before Printing
+
+- [ ] Title visible and readable from 20+ feet
+- [ ] Body text minimum 24pt, ideally 30pt+
+- [ ] High contrast (4.5:1 minimum) throughout
+- [ ] Color-blind friendly palette
+- [ ] Less than 800 words total
+- [ ] White space around all elements
+- [ ] Consistent alignment and spacing
+- [ ] All figures high resolution (300+ DPI)
+- [ ] Figure labels readable (18pt+ minimum)
+- [ ] No orphaned text or awkward breaks
+- [ ] Contact information included
+- [ ] QR codes tested and functional
+- [ ] Consistent font usage (2-3 families max)
+- [ ] All acronyms defined
+- [ ] Proper institutional branding/logos
+- [ ] Print test at 25% scale for readability check
+
+### Content Review
+
+- [ ] Clear narrative arc (problem → approach → findings → impact)
+- [ ] 1-3 main messages clearly communicated
+- [ ] Methods concise but reproducible
+- [ ] Results visually presented (not just text)
+- [ ] Conclusions actionable and clear
+- [ ] References cited appropriately
+- [ ] No typos or grammatical errors
+- [ ] Figures have descriptive captions
+- [ ] Data visualizations are clear and honest
+- [ ] Statistical significance properly indicated
+
+## Evidence-Based Design Recommendations
+
+Research on poster effectiveness shows:
+
+**Findings from Studies**:
+1. **Viewers spend 3-5 minutes average** on posters
+ - Design for scanning, not deep reading
+ - Most important info must be visible immediately
+
+2. **Visual content processed 60,000× faster** than text
+ - Use figures, not paragraphs, to convey key findings
+ - Images attract attention first
+
+3. **High contrast improves recall** by 40%
+ - Dark on light > light on dark for comprehension
+ - Color contrast aids memory retention
+
+4. **White space increases comprehension** by 20%
+ - Don't fear empty space
+ - Margins and padding are essential
+
+5. **Three-column layouts most effective** for portrait posters
+ - Balanced visual weight
+ - Natural reading flow
+
+6. **QR codes increase engagement** by 30%
+ - Provide digital access to full paper
+ - Link to videos, code repositories, data
+
+## Resources and Tools
+
+### Color Tools
+- **Coolors.co**: Generate color palettes
+- **Adobe Color**: Color wheel and accessibility checker
+- **ColorBrewer**: Scientific visualization palettes
+- **WebAIM Contrast Checker**: Test contrast ratios
+
+### Design Resources
+- **Canva**: Poster mockups and inspiration
+- **Figma**: Design prototypes before LaTeX
+- **Noun Project**: Icons and graphics
+- **Font Awesome**: Icon fonts for LaTeX
+
+### Testing Tools
+- **Coblis**: Color blindness simulator
+- **Vischeck**: Another color blindness checker
+- **Accessibility Checker**: WCAG compliance
+
+### LaTeX Packages
+- `xcolor`: Extended color support
+- `tcolorbox`: Colored boxes and frames
+- `fontawesome5`: Icon fonts
+- `qrcode`: QR code generation
+- `tikz`: Custom graphics
+
+## Conclusion
+
+Effective poster design requires balancing aesthetics, readability, and scientific content. Follow these core principles:
+
+1. **Less is more**: Prioritize key messages over comprehensive detail
+2. **Size matters**: Make text large enough to read from distance
+3. **Contrast is critical**: Ensure all text is highly readable
+4. **Accessibility first**: Design for diverse audiences
+5. **Visual hierarchy**: Guide viewers through content logically
+6. **Test early**: Print at reduced scale and gather feedback
+
+Remember: A poster is an advertisement for your research and a conversation starter—not a substitute for reading the full paper.
+
diff --git a/scientific-skills/latex-posters/references/poster_layout_design.md b/scientific-skills/latex-posters/references/poster_layout_design.md
new file mode 100644
index 0000000..b00a584
--- /dev/null
+++ b/scientific-skills/latex-posters/references/poster_layout_design.md
@@ -0,0 +1,900 @@
+# Poster Layout and Design Guide
+
+## Overview
+
+Effective poster layout organizes content for maximum impact and comprehension. This guide covers grid systems, spatial organization, visual flow, and layout patterns for research posters.
+
+## Grid Systems and Column Layouts
+
+### Common Grid Patterns
+
+#### 1. Two-Column Layout
+
+**Characteristics**:
+- Simple, traditional structure
+- Easy to design and execute
+- Clear narrative flow
+- Good for text-heavy content
+- Best for A1 size or smaller
+
+**Content Organization**:
+```
++-------------------------+
+| Title/Header |
++-------------------------+
+| Column 1 | Column 2 |
+| | |
+| Intro | Results |
+| | |
+| Methods | Discussion |
+| | |
+| | Conclusions |
++-------------------------+
+| References/Contact |
++-------------------------+
+```
+
+**LaTeX Implementation (beamerposter)**:
+```latex
+\begin{columns}[t]
+ \begin{column}{.48\linewidth}
+ \begin{block}{Introduction}
+ % Content
+ \end{block}
+ \begin{block}{Methods}
+ % Content
+ \end{block}
+ \end{column}
+
+ \begin{column}{.48\linewidth}
+ \begin{block}{Results}
+ % Content
+ \end{block}
+ \begin{block}{Conclusions}
+ % Content
+ \end{block}
+ \end{column}
+\end{columns}
+```
+
+**Best For**:
+- Small posters (A1, A2)
+- Narrative-heavy content
+- Simple comparisons (before/after, control/treatment)
+- Linear storytelling
+
+**Limitations**:
+- Limited space for multiple results
+- Can appear basic or dated
+- Less visual variety
+
+#### 2. Three-Column Layout (Most Popular)
+
+**Characteristics**:
+- Balanced, professional appearance
+- Optimal for A0 posters
+- Versatile content distribution
+- Natural visual rhythm
+- Industry standard
+
+**Content Organization**:
+```
++--------------------------------+
+| Title/Header |
++--------------------------------+
+| Column 1 | Column 2 | Column 3|
+| | | |
+| Intro | Results | Results |
+| | (Fig 1) | (Fig 2) |
+| Methods | | |
+| | Results | Discuss |
+| Methods | (Fig 3) | |
+| (cont.) | | Concl. |
++--------------------------------+
+| Acknowledgments/Refs |
++--------------------------------+
+```
+
+**LaTeX Implementation (tikzposter)**:
+```latex
+\begin{columns}
+ \column{0.33}
+ \block{Introduction}{...}
+ \block{Methods}{...}
+
+ \column{0.33}
+ \block{Results Part 1}{...}
+ \block{Results Part 2}{...}
+
+ \column{0.33}
+ \block{Results Part 3}{...}
+ \block{Discussion}{...}
+ \block{Conclusions}{...}
+\end{columns}
+```
+
+**Best For**:
+- Standard A0 conference posters
+- Multiple results/figures (4-6)
+- Balanced content distribution
+- Professional academic presentations
+
+**Strengths**:
+- Visual balance and symmetry
+- Adequate space for text and figures
+- Clear section delineation
+- Easy to scan left-to-right
+
+#### 3. Four-Column Layout
+
+**Characteristics**:
+- Information-dense
+- Modern, structured appearance
+- Best for large posters (>A0)
+- Requires careful design
+- More complex to balance
+
+**Content Organization**:
+```
++----------------------------------------+
+| Title/Header |
++----------------------------------------+
+| Col 1 | Col 2 | Col 3 | Col 4 |
+| | | | |
+| Intro | Method | Results | Results |
+| | (Flow) | (Fig 1) | (Fig 3) |
+| Motiv. | | | |
+| | Method | Results | Discuss. |
+| Hypoth.| (Stats)| (Fig 2) | |
+| | | | Concl. |
++----------------------------------------+
+| References/Contact |
++----------------------------------------+
+```
+
+**LaTeX Implementation (baposter)**:
+```latex
+\begin{poster}{columns=4, colspacing=1em, ...}
+
+ \headerbox{Intro}{name=intro, column=0, row=0}{...}
+ \headerbox{Methods}{name=methods, column=1, row=0}{...}
+ \headerbox{Results 1}{name=res1, column=2, row=0}{...}
+ \headerbox{Results 2}{name=res2, column=3, row=0}{...}
+
+ % Continue with below=... for stacking
+
+\end{poster}
+```
+
+**Best For**:
+- Large format posters (48×72")
+- Data-heavy presentations
+- Comparison studies (multiple conditions)
+- Engineering/technical posters
+
+**Challenges**:
+- Can appear crowded
+- Requires more white space management
+- Harder to achieve visual balance
+- Risk of overwhelming viewers
+
+#### 4. Asymmetric Layouts
+
+**Characteristics**:
+- Dynamic, modern appearance
+- Flexible content arrangement
+- Emphasizes hierarchy
+- Requires design expertise
+- Best for creative fields
+
+**Example Pattern**:
+```
++--------------------------------+
+| Title/Header |
++--------------------------------+
+| Wide Column | Narrow Column |
+| (66%) | (33%) |
+| | |
+| Intro + | Key |
+| Methods | Figure |
+| (narrative) | (emphasized) |
+| | |
++--------------------------------+
+| Results (spanning full width) |
++--------------------------------+
+| Discussion | Conclusions |
+| (50%) | (50%) |
++--------------------------------+
+```
+
+**LaTeX Implementation (tikzposter)**:
+```latex
+\begin{columns}
+ \column{0.65}
+ \block{Introduction and Methods}{
+ % Combined narrative section
+ }
+
+ \column{0.35}
+ \block{}{
+ % Key figure with minimal text
+ \includegraphics[width=\linewidth]{key-figure.pdf}
+ }
+\end{columns}
+
+\block[width=1.0\linewidth]{Results}{
+ % Full-width results section
+}
+```
+
+**Best For**:
+- Design-oriented conferences
+- Single key finding with supporting content
+- Modern, non-traditional fields
+- Experienced poster designers
+
+### Grid Alignment Principles
+
+**Baseline Grid**:
+- Establish invisible horizontal lines
+- Align all text blocks to grid
+- Typical spacing: 5mm or 10mm increments
+- Creates visual rhythm and professionalism
+
+**Column Grid**:
+- Divide width into equal units (12, 16, or 24 units common)
+- Elements span multiple units
+- Allows flexible but structured layouts
+
+**Example 12-Column Grid**:
+```
+| 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |10 |11 |12 |
+|-------|-------|-------|-------|-------|-------|
+| Block spanning 6 units| Block spanning 6 units|
+| Block spanning 12 units |
+| 4 units | 8 units (emphasized) |
+```
+
+**LaTeX Grid Helper**:
+```latex
+% Debug grid overlay (remove for final version)
+\usepackage{tikz}
+\AddToShipoutPictureBG{
+ \begin{tikzpicture}[remember picture, overlay]
+ \draw[help lines, step=5cm, very thin, gray!30]
+ (current page.south west) grid (current page.north east);
+ \end{tikzpicture}
+}
+```
+
+## Visual Flow and Reading Patterns
+
+### Z-Pattern (Landscape Posters)
+
+Viewers' eyes naturally follow a Z-shape on landscape layouts:
+
+```
+START → → → → → → → → → → → → → → TOP RIGHT
+ ↓ ↓
+ ↓ ↓
+MIDDLE LEFT → → → → → → → → → MIDDLE RIGHT
+ ↓ ↓
+ ↓ ↓
+BOTTOM LEFT → → → → → → → → → → → → END
+```
+
+**Design Strategy**:
+1. **Top-left**: Title and introduction (entry point)
+2. **Top-right**: Institution logo, QR code
+3. **Center**: Key result or main figure
+4. **Bottom-right**: Conclusions and contact (exit point)
+
+**Content Placement**:
+- Critical information at corners and center
+- Support information along diagonal paths
+- Use arrows or visual cues to reinforce flow
+
+### F-Pattern (Portrait Posters)
+
+Portrait posters follow F-shaped eye movement:
+
+```
+TITLE → → → → → → → → → → → →
+ ↓
+INTRO → → → →
+ ↓
+METHODS
+ ↓
+RESULTS → → →
+ ↓
+RESULTS (cont.)
+ ↓
+DISCUSSION
+ ↓
+CONCLUSIONS → → → → → → → → →
+```
+
+**Design Strategy**:
+1. Place engaging content at top-left
+2. Use section headers to create horizontal scan points
+3. Most important figures in upper-middle area
+4. Conclusions visible without scrolling (if digital) or from distance
+
+### Gutenberg Diagram
+
+Classic newspaper layout principle:
+
+```
++------------------+------------------+
+| PRIMARY AREA | STRONG FALLOW |
+| (most attention) | (moderate attn) |
+| ↓ | ↓ |
++------------------+------------------+
+| WEAK FALLOW | TERMINAL AREA |
+| (least attention)| (final resting) |
+| | ↑ |
++------------------+------------------+
+```
+
+**Optimization**:
+- **Primary Area** (top-left): Introduction, problem statement
+- **Strong Fallow** (top-right): Supporting figure, logo
+- **Weak Fallow** (bottom-left): Methods details, references
+- **Terminal Area** (bottom-right): Conclusions, take-home message
+
+### Directional Cues
+
+Guide viewers explicitly through content:
+
+**Numerical Ordering**:
+```latex
+\block{❶ Introduction}{...}
+\block{❷ Methods}{...}
+\block{❸ Results}{...}
+\block{❹ Conclusions}{...}
+```
+
+**Arrows and Lines**:
+```latex
+\begin{tikzpicture}
+ \node[block] (intro) {Introduction};
+ \node[block, right=of intro] (methods) {Methods};
+ \node[block, right=of methods] (results) {Results};
+ \draw[->, thick, blue] (intro) -- (methods);
+ \draw[->, thick, blue] (methods) -- (results);
+\end{tikzpicture}
+```
+
+**Color Progression**:
+- Light to dark shades indicating progression
+- Cool to warm colors showing importance increase
+- Consistent color for related sections
+
+## Spatial Organization Strategies
+
+### Header/Title Area
+
+**Typical Size**: 10-15% of total poster height
+
+**Essential Elements**:
+- **Title**: Concise, descriptive (10-15 words max)
+- **Authors**: Full names, presenting author emphasized
+- **Affiliations**: Institutions, departments
+- **Logos**: University, funding agencies (2-4 max)
+- **Conference info** (optional): Name, date, location
+
+**Layout Options**:
+
+**Centered**:
+```
++----------------------------------------+
+| [Logo] POSTER TITLE HERE [Logo]|
+| Authors and Affiliations |
+| email@university.edu |
++----------------------------------------+
+```
+
+**Left-aligned**:
+```
++----------------------------------------+
+| POSTER TITLE HERE [Logo] |
+| Authors and Affiliations [Logo] |
++----------------------------------------+
+```
+
+**Split**:
+```
++----------------------------------------+
+| [Logo] | Authors & Affil. |
+| POSTER TITLE | email@edu |
+| | [QR Code] |
++----------------------------------------+
+```
+
+**LaTeX Header (beamerposter)**:
+```latex
+\begin{columns}[T]
+ \begin{column}{.15\linewidth}
+ \includegraphics[width=\linewidth]{logo1.pdf}
+ \end{column}
+
+ \begin{column}{.7\linewidth}
+ \centering
+ {\VeryHuge\textbf{Your Research Title Here}}\\[0.5cm]
+ {\Large Author One\textsuperscript{1}, Author Two\textsuperscript{2}}\\[0.3cm]
+ {\normalsize \textsuperscript{1}University A, \textsuperscript{2}University B}
+ \end{column}
+
+ \begin{column}{.15\linewidth}
+ \includegraphics[width=\linewidth]{logo2.pdf}
+ \end{column}
+\end{columns}
+```
+
+### Main Content Area
+
+**Typical Size**: 70-80% of total poster
+
+**Organization Principles**:
+
+**1. Top-to-Bottom Flow**:
+```
+Introduction/Background
+ ↓
+Methods/Approach
+ ↓
+Results (Multiple panels)
+ ↓
+Discussion/Conclusions
+```
+
+**2. Left-to-Right, Top-to-Bottom**:
+```
+[Intro] [Results 1] [Results 3]
+[Methods] [Results 2] [Discussion]
+```
+
+**3. Centralized Main Figure**:
+```
+[Intro] [Main Figure] [Discussion]
+[Methods] (center) [Conclusions]
+```
+
+**Section Sizing**:
+- Introduction: 10-15% of content area
+- Methods: 15-20%
+- Results: 40-50% (largest section)
+- Discussion/Conclusions: 15-20%
+
+### Footer Area
+
+**Typical Size**: 5-10% of total poster height
+
+**Common Elements**:
+- References (abbreviated, 5-10 key citations)
+- Acknowledgments (funding, collaborators)
+- Contact information
+- QR codes (paper, code, data)
+- Social media handles (optional)
+- Conference hashtags
+
+**Layout**:
+```
++----------------------------------------+
+| References: 1. Author (2023) ... | 📱 |
+| Acknowledgments: Funded by ... | QR |
+| Contact: name@email.edu | Code |
++----------------------------------------+
+```
+
+**LaTeX Footer**:
+```latex
+\begin{block}{}
+ \footnotesize
+ \begin{columns}[T]
+ \begin{column}{0.7\linewidth}
+ \textbf{References}
+ \begin{enumerate}
+ \item Author A et al. (2023). Journal. doi:...
+ \item Author B et al. (2024). Conference.
+ \end{enumerate}
+
+ \textbf{Acknowledgments}
+ This work was supported by Grant XYZ.
+
+ \textbf{Contact}: firstname.lastname@university.edu
+ \end{column}
+
+ \begin{column}{0.25\linewidth}
+ \centering
+ \qrcode[height=3cm]{https://doi.org/10.1234/paper}\\
+ \tiny Scan for full paper
+ \end{column}
+ \end{columns}
+\end{block}
+```
+
+## White Space Management
+
+### Margins and Padding
+
+**Outer Margins**:
+- Minimum: 2-3cm (0.75-1 inch)
+- Recommended: 3-5cm (1-2 inches)
+- Prevents edge trimming issues in printing
+- Provides visual breathing room
+
+**Inner Spacing**:
+- Between columns: 1-2cm
+- Between blocks: 1-2cm
+- Inside blocks (padding): 0.5-1.5cm
+- Around figures: 0.5-1cm
+
+**LaTeX Margin Control**:
+```latex
+% beamerposter
+\usepackage[size=a0, scale=1.4]{beamerposter}
+\setbeamersize{text margin left=3cm, text margin right=3cm}
+
+% tikzposter
+\documentclass[..., margin=30mm, innermargin=15mm]{tikzposter}
+
+% baposter
+\begin{poster}{
+ colspacing=1.5em, % Horizontal spacing
+ ...
+}
+```
+
+### Active White Space vs. Passive White Space
+
+**Active White Space**: Intentionally placed for specific purpose
+- Around key figures (draws attention)
+- Between major sections (creates clear separation)
+- Above/below titles (emphasizes hierarchy)
+
+**Passive White Space**: Natural result of layout
+- Margins and borders
+- Line spacing
+- Gaps between elements
+
+**Balance**: Aim for 30-40% white space overall
+
+### Visual Breathing Room
+
+**Avoid**:
+- ❌ Elements touching edges
+- ❌ Text blocks directly adjacent
+- ❌ Figures without surrounding space
+- ❌ Cramped, claustrophobic feel
+
+**Implement**:
+- ✅ Clear separation between sections
+- ✅ Space around focal points
+- ✅ Generous padding inside boxes
+- ✅ Balanced distribution of content
+
+## Block and Box Design
+
+### Block Types and Functions
+
+**Title Block**: Poster header
+- Full width, top position
+- High visual weight
+- Contains identifying information
+
+**Content Blocks**: Main sections
+- Column-based or free-floating
+- Hierarchical sizing (larger = more important)
+- Clear headers and structure
+
+**Callout Blocks**: Emphasized information
+- Key findings or quotes
+- Different color or style
+- Visually distinct
+
+**Reference Blocks**: Supporting info
+- Footer position
+- Smaller, less prominent
+- Informational, not critical
+
+### Block Styling Options
+
+**Border Styles**:
+```latex
+% Rounded corners (friendly, modern)
+\begin{block}{Title}
+ % beamerposter with rounded
+ \setbeamertemplate{block begin}[rounded]
+
+% Sharp corners (formal, traditional)
+ \setbeamertemplate{block begin}[default]
+
+% No border (minimal, clean)
+ \setbeamercolor{block title}{bg=white, fg=black}
+ \setbeamercolor{block body}{bg=white, fg=black}
+```
+
+**Shadow and Depth**:
+```latex
+% tikzposter shadow
+\tikzset{
+ block/.append style={
+ drop shadow={shadow xshift=2mm, shadow yshift=-2mm}
+ }
+}
+
+% tcolorbox drop shadow
+\usepackage{tcolorbox}
+\begin{tcolorbox}[enhanced, drop shadow]
+ Content with shadow
+\end{tcolorbox}
+```
+
+**Background Shading**:
+- **Solid**: Clean, professional
+- **Gradient**: Modern, dynamic
+- **Transparent**: Layered, sophisticated
+
+### Relationship and Grouping
+
+**Visual Grouping Techniques**:
+
+**1. Proximity**: Place related items close
+```
+[Intro Text]
+[Related Figure]
+ ↓ grouped
+[Methods Text]
+[Methods Diagram]
+```
+
+**2. Color Coding**: Use color to show relationships
+- All "Methods" blocks in blue
+- All "Results" blocks in green
+- Conclusions in orange
+
+**3. Borders**: Enclose related elements
+```latex
+\begin{tcolorbox}[title=Experimental Pipeline]
+ \begin{enumerate}
+ \item Sample preparation
+ \item Data collection
+ \item Analysis
+ \end{enumerate}
+\end{tcolorbox}
+```
+
+**4. Alignment**: Aligned elements appear related
+```
+[Block A Left-aligned]
+[Block B Left-aligned]
+ vs.
+[Block C Centered]
+```
+
+## Responsive and Adaptive Layouts
+
+### Designing for Different Poster Sizes
+
+**Scaling Strategy**:
+- Design for target size (e.g., A0)
+- Test at other common sizes (A1, 36×48")
+- Use relative sizing (percentages, not absolute)
+
+**Font Scaling**:
+```latex
+% Scale fonts proportionally
+\usepackage[size=a0, scale=1.4]{beamerposter} % A0 at 140%
+\usepackage[size=a1, scale=1.0]{beamerposter} % A1 at 100%
+
+% Or define sizes relatively
+\newcommand{\titlesize}{\fontsize{96}{110}\selectfont}
+\newcommand{\headersize}{\fontsize{60}{72}\selectfont}
+```
+
+**Content Adaptation**:
+- **A0 (full)**: All content, 5-6 figures
+- **A1 (reduced)**: Condense to 3-4 main figures
+- **A2 (compact)**: Key finding only, 1-2 figures
+
+### Portrait vs. Landscape Orientation
+
+**Portrait (Vertical)**:
+- **Pros**: Traditional, more common stands, natural reading flow
+- **Cons**: Less width for figures, can feel cramped
+- **Best for**: Text-heavy posters, multi-section flow, conferences
+
+**Landscape (Horizontal)**:
+- **Pros**: Wide figures, natural for timelines, modern feel
+- **Cons**: Harder to read from distance, less common
+- **Best for**: Timelines, wide data visualizations, non-traditional venues
+
+**LaTeX Orientation**:
+```latex
+% Portrait
+\usepackage[size=a0, orientation=portrait]{beamerposter}
+\documentclass[..., portrait]{tikzposter}
+
+% Landscape
+\usepackage[size=a0, orientation=landscape]{beamerposter}
+\documentclass[..., landscape]{tikzposter}
+```
+
+## Layout Patterns by Research Type
+
+### Experimental Research
+
+**Typical Flow**:
+```
+[Title and Authors]
++---------------------------+
+| Background | Methods |
+| Problem | (Diagram) |
++---------------------------+
+| Results (Figure 1) |
+| Results (Figure 2) |
++---------------------------+
+| Discussion | Conclusions |
+| Limitations| Future Work |
++---------------------------+
+[References and Contact]
+```
+
+**Emphasis**: Visual results, clear methodology
+
+### Computational/Modeling
+
+**Typical Flow**:
+```
+[Title and Authors]
++---------------------------+
+| Motivation | Algorithm |
+| | (Flowchart) |
++---------------------------+
+| Implementation Details |
++---------------------------+
+| Results | Results |
+| (Benchmark)| (Comparison) |
++---------------------------+
+| Conclusions| Code QR |
++---------------------------+
+[GitHub, Docker, Documentation]
+```
+
+**Emphasis**: Algorithm clarity, reproducibility
+
+### Clinical/Medical
+
+**Typical Flow**:
+```
+[Title and Authors]
++---------------------------+
+| Background | Methods |
+| Clinical | - Design |
+| Need | - Population |
+| | - Outcomes |
++---------------------------+
+| Results | |
+| (Primary Outcome) | Key|
+| | Fig|
++---------------------------+
+| Discussion | Clinical |
+| | Implications |
++---------------------------+
+[Trial Registration, Ethics, Funding]
+```
+
+**Emphasis**: Patient outcomes, clinical relevance
+
+### Review/Meta-Analysis
+
+**Typical Flow**:
+```
+[Title and Authors]
++---------------------------+
+| Research | Search |
+| Question | Strategy |
+| | (PRISMA Flow) |
++---------------------------+
+| Included Studies Overview |
++---------------------------+
+| Findings | Findings |
+| (Theme 1) | (Theme 2) |
++---------------------------+
+| Synthesis | Gaps & |
+| | Future Needs |
++---------------------------+
+[Systematic Review Registration]
+```
+
+**Emphasis**: Comprehensive coverage, synthesis
+
+## Layout Testing and Iteration
+
+### Design Iteration Process
+
+**1. Sketch Phase**:
+- Hand-draw rough layout
+- Experiment with different arrangements
+- Mark primary, secondary, tertiary content
+
+**2. Digital Mockup**:
+- Create low-fidelity version in LaTeX
+- Use placeholder text/figures
+- Test different grid systems
+
+**3. Content Integration**:
+- Replace placeholders with actual content
+- Adjust spacing and sizing
+- Refine visual hierarchy
+
+**4. Refinement**:
+- Fine-tune alignment
+- Balance visual weight
+- Optimize white space
+
+**5. Testing**:
+- Print at reduced scale (25%)
+- View from distance
+- Get colleague feedback
+
+### Feedback Checklist
+
+**Visual Balance**:
+- [ ] No single area feels too heavy or too light
+- [ ] Color distributed evenly across poster
+- [ ] Text and figures balanced
+- [ ] White space well-distributed
+
+**Hierarchy and Flow**:
+- [ ] Clear entry point (title visible)
+- [ ] Logical reading path
+- [ ] Section relationships clear
+- [ ] Conclusions easy to find
+
+**Technical Execution**:
+- [ ] Consistent alignment
+- [ ] Uniform spacing
+- [ ] Professional appearance
+- [ ] No awkward breaks or orphans
+
+## Common Layout Mistakes
+
+**1. Unbalanced Visual Weight**
+- ❌ All content on left, empty right side
+- ❌ Large figure dominating, tiny text elsewhere
+- ✅ Distribute content evenly across poster
+
+**2. Inconsistent Spacing**
+- ❌ Random gaps between blocks
+- ❌ Elements touching in some places, spaced in others
+- ✅ Use consistent spacing values throughout
+
+**3. Poor Column Width**
+- ❌ Extremely narrow columns (hard to read)
+- ❌ Very wide columns (eye tracking difficult)
+- ✅ Optimal: 40-80 characters per line
+
+**4. Ignoring Grid**
+- ❌ Random placement of elements
+- ❌ Misaligned blocks
+- ✅ Align to invisible grid, consistent positioning
+
+**5. Overcrowding**
+- ❌ No white space, cramped feel
+- ❌ Trying to fit too much content
+- ✅ Generous margins, clear separation
+
+## Conclusion
+
+Effective layout design:
+- Uses appropriate grid systems (2, 3, or 4 columns)
+- Follows natural eye movement patterns
+- Maintains visual balance and hierarchy
+- Provides adequate white space
+- Groups related content clearly
+- Adapts to different poster sizes and orientations
+
+Remember: Layout should support content, not compete with it. When viewers focus on your research rather than your design, you've succeeded.
+
diff --git a/scientific-skills/latex-posters/scripts/review_poster.sh b/scientific-skills/latex-posters/scripts/review_poster.sh
new file mode 100755
index 0000000..1081be6
--- /dev/null
+++ b/scientific-skills/latex-posters/scripts/review_poster.sh
@@ -0,0 +1,214 @@
+#!/bin/bash
+
+# Poster PDF Quality Check Script
+# Usage: ./review_poster.sh poster.pdf
+
+# Colors for output
+RED='\033[0;31m'
+GREEN='\033[0;32m'
+YELLOW='\033[1;33m'
+BLUE='\033[0;34m'
+NC='\033[0m' # No Color
+
+# Check if file argument provided
+if [ $# -eq 0 ]; then
+ echo -e "${RED}Error: No file specified${NC}"
+ echo "Usage: $0 "
+ exit 1
+fi
+
+POSTER_FILE="$1"
+
+# Check if file exists
+if [ ! -f "$POSTER_FILE" ]; then
+ echo -e "${RED}Error: File '$POSTER_FILE' not found${NC}"
+ exit 1
+fi
+
+echo -e "${BLUE}═══════════════════════════════════════════════${NC}"
+echo -e "${BLUE} Poster PDF Quality Check${NC}"
+echo -e "${BLUE}═══════════════════════════════════════════════${NC}"
+echo ""
+echo -e "${GREEN}File:${NC} $POSTER_FILE"
+echo ""
+
+# Function to check if command exists
+command_exists() {
+ command -v "$1" >/dev/null 2>&1
+}
+
+# 1. Page Size Check
+echo -e "${YELLOW}[1] Page Dimensions:${NC}"
+if command_exists pdfinfo; then
+ PAGE_SIZE=$(pdfinfo "$POSTER_FILE" 2>/dev/null | grep "Page size")
+ if [ -n "$PAGE_SIZE" ]; then
+ echo " $PAGE_SIZE"
+
+ # Extract dimensions and check common sizes
+ WIDTH=$(echo "$PAGE_SIZE" | awk '{print $3}')
+ HEIGHT=$(echo "$PAGE_SIZE" | awk '{print $5}')
+
+ # Check against common poster sizes (approximate)
+ if [ "$WIDTH" = "2384" ] && [ "$HEIGHT" = "3370" ]; then
+ echo -e " ${GREEN}✓ Detected: A0 Portrait${NC}"
+ elif [ "$WIDTH" = "3370" ] && [ "$HEIGHT" = "2384" ]; then
+ echo -e " ${GREEN}✓ Detected: A0 Landscape${NC}"
+ elif [ "$WIDTH" = "1684" ] && [ "$HEIGHT" = "2384" ]; then
+ echo -e " ${GREEN}✓ Detected: A1 Portrait${NC}"
+ elif [ "$WIDTH" = "2592" ] && [ "$HEIGHT" = "3456" ]; then
+ echo -e " ${GREEN}✓ Detected: 36×48 inches Portrait${NC}"
+ else
+ echo -e " ${YELLOW}⚠ Non-standard size detected${NC}"
+ fi
+ else
+ echo -e " ${RED}✗ Could not extract page size${NC}"
+ fi
+else
+ echo -e " ${YELLOW}⚠ pdfinfo not installed (install: brew install poppler or apt-get install poppler-utils)${NC}"
+fi
+echo ""
+
+# 2. Page Count
+echo -e "${YELLOW}[2] Page Count:${NC}"
+if command_exists pdfinfo; then
+ PAGE_COUNT=$(pdfinfo "$POSTER_FILE" 2>/dev/null | grep "Pages" | awk '{print $2}')
+ if [ "$PAGE_COUNT" = "1" ]; then
+ echo -e " ${GREEN}✓ Single page (correct for poster)${NC}"
+ else
+ echo -e " ${RED}✗ Multiple pages detected: $PAGE_COUNT${NC}"
+ echo -e " ${YELLOW} Posters should be single page${NC}"
+ fi
+else
+ echo -e " ${YELLOW}⚠ pdfinfo not installed${NC}"
+fi
+echo ""
+
+# 3. File Size
+echo -e "${YELLOW}[3] File Size:${NC}"
+if command_exists ls; then
+ FILE_SIZE=$(ls -lh "$POSTER_FILE" | awk '{print $5}')
+ FILE_SIZE_BYTES=$(ls -l "$POSTER_FILE" | awk '{print $5}')
+ echo " Size: $FILE_SIZE"
+
+ # Check if file is too large for email
+ if [ "$FILE_SIZE_BYTES" -gt 52428800 ]; then # 50MB
+ echo -e " ${YELLOW}⚠ Large file (>50MB) - may need compression for email${NC}"
+ echo -e " ${BLUE} Compress with: gs -sDEVICE=pdfwrite -dPDFSETTINGS=/printer -dNOPAUSE -dQUIET -dBATCH -sOutputFile=compressed.pdf $POSTER_FILE${NC}"
+ elif [ "$FILE_SIZE_BYTES" -lt 1048576 ]; then # 1MB
+ echo -e " ${YELLOW}⚠ Small file - check image quality${NC}"
+ else
+ echo -e " ${GREEN}✓ Reasonable file size${NC}"
+ fi
+fi
+echo ""
+
+# 4. Font Embedding Check
+echo -e "${YELLOW}[4] Font Embedding:${NC}"
+if command_exists pdffonts; then
+ echo " Checking first 20 fonts..."
+ FONT_OUTPUT=$(pdffonts "$POSTER_FILE" 2>/dev/null | head -21)
+ echo "$FONT_OUTPUT" | tail -20 | while IFS= read -r line; do
+ echo " $line"
+ done
+
+ # Check for non-embedded fonts
+ NON_EMBEDDED=$(echo "$FONT_OUTPUT" | tail -n +3 | awk '{if ($4 == "no") print $0}')
+ if [ -n "$NON_EMBEDDED" ]; then
+ echo -e " ${RED}✗ Some fonts are NOT embedded (printing may fail)${NC}"
+ echo -e " ${BLUE} Fix: Recompile with 'pdflatex -dEmbedAllFonts=true poster.tex'${NC}"
+ else
+ echo -e " ${GREEN}✓ All fonts appear to be embedded${NC}"
+ fi
+else
+ echo -e " ${YELLOW}⚠ pdffonts not installed (install: brew install poppler or apt-get install poppler-utils)${NC}"
+fi
+echo ""
+
+# 5. Image Quality Check
+echo -e "${YELLOW}[5] Image Quality:${NC}"
+if command_exists pdfimages; then
+ IMAGE_COUNT=$(pdfimages -list "$POSTER_FILE" 2>/dev/null | tail -n +3 | wc -l | tr -d ' ')
+ if [ "$IMAGE_COUNT" -gt 0 ]; then
+ echo " Found $IMAGE_COUNT image(s)"
+ echo " Image details:"
+ pdfimages -list "$POSTER_FILE" 2>/dev/null | head -20
+
+ # Note: DPI calculation would require page size knowledge
+ echo -e " ${BLUE} Verify images are at least 300 DPI for printing${NC}"
+ echo -e " ${BLUE} Formula: DPI = pixels / (inches in poster)${NC}"
+ else
+ echo -e " ${YELLOW}⚠ No images found${NC}"
+ fi
+else
+ echo -e " ${YELLOW}⚠ pdfimages not installed (install: brew install poppler or apt-get install poppler-utils)${NC}"
+fi
+echo ""
+
+# 6. Manual Checks Required
+echo -e "${YELLOW}[6] Manual Visual Inspection Required:${NC}"
+echo ""
+echo -e "${BLUE}Layout and Spacing:${NC}"
+echo " [ ] Content fills entire page (no large white margins)"
+echo " [ ] Consistent spacing between columns"
+echo " [ ] Consistent spacing between blocks/sections"
+echo " [ ] All elements aligned properly"
+echo " [ ] No overlapping text or figures"
+echo ""
+
+echo -e "${BLUE}Typography:${NC}"
+echo " [ ] Title visible and large (72pt+)"
+echo " [ ] Section headers readable (48-72pt)"
+echo " [ ] Body text readable (24-36pt minimum)"
+echo " [ ] No text cutoff or running off edges"
+echo " [ ] Consistent font usage"
+echo ""
+
+echo -e "${BLUE}Visual Elements:${NC}"
+echo " [ ] All figures display correctly"
+echo " [ ] No pixelated or blurry images"
+echo " [ ] Figure captions present and readable"
+echo " [ ] Colors render as expected"
+echo " [ ] Logos display clearly"
+echo " [ ] QR codes visible and scannable"
+echo ""
+
+echo -e "${BLUE}Content:${NC}"
+echo " [ ] All sections present (Intro, Methods, Results, Conclusions)"
+echo " [ ] References included"
+echo " [ ] Contact information visible"
+echo " [ ] No placeholder text (Lorem ipsum, TODO, etc.)"
+echo ""
+
+# 7. Recommended Tests
+echo -e "${YELLOW}[7] Recommended Next Steps:${NC}"
+echo ""
+echo -e "${BLUE}Test Print:${NC}"
+echo " • Print at 25% scale (A0→A4, 36×48→Letter)"
+echo " • Check readability from 2-3 feet"
+echo " • Verify colors printed accurately"
+echo ""
+
+echo -e "${BLUE}Digital Checks:${NC}"
+echo " • View at 100% zoom in PDF viewer"
+echo " • Test on different screens/devices"
+echo " • Verify QR codes work with scanner app"
+echo ""
+
+echo -e "${BLUE}Proofreading:${NC}"
+echo " • Spell-check all text"
+echo " • Verify author names and affiliations"
+echo " • Confirm all statistics and numbers"
+echo " • Ask colleague to review"
+echo ""
+
+# 8. Summary
+echo -e "${BLUE}═══════════════════════════════════════════════${NC}"
+echo -e "${BLUE} Quality Check Complete${NC}"
+echo -e "${BLUE}═══════════════════════════════════════════════${NC}"
+echo ""
+echo -e "Review the checks above and complete manual verification."
+echo -e "For full checklist, see: ${BLUE}assets/poster_quality_checklist.md${NC}"
+echo ""
+
+exit 0
+
diff --git a/scientific-skills/literature-review/SKILL.md b/scientific-skills/literature-review/SKILL.md
new file mode 100644
index 0000000..9a55eea
--- /dev/null
+++ b/scientific-skills/literature-review/SKILL.md
@@ -0,0 +1,584 @@
+---
+name: literature-review
+description: Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should be used when conducting systematic literature reviews, meta-analyses, research synthesis, or comprehensive literature searches across biomedical, scientific, and technical domains. Creates professionally formatted markdown documents and PDFs with verified citations in multiple citation styles (APA, Nature, Vancouver, etc.).
+allowed-tools: [Read, Write, Edit, Bash]
+---
+
+# Literature Review
+
+## Overview
+
+Conduct systematic, comprehensive literature reviews following rigorous academic methodology. Search multiple literature databases, synthesize findings thematically, verify all citations for accuracy, and generate professional output documents in markdown and PDF formats.
+
+This skill integrates with multiple scientific skills for database access (gget, bioservices, datacommons-client) and provides specialized tools for citation verification, result aggregation, and document generation.
+
+## When to Use This Skill
+
+Use this skill when:
+- Conducting a systematic literature review for research or publication
+- Synthesizing current knowledge on a specific topic across multiple sources
+- Performing meta-analysis or scoping reviews
+- Writing the literature review section of a research paper or thesis
+- Investigating the state of the art in a research domain
+- Identifying research gaps and future directions
+- Requiring verified citations and professional formatting
+
+## Visual Enhancement with Scientific Schematics
+
+**⚠️ MANDATORY: Every literature review MUST include at least 1-2 AI-generated figures using the scientific-schematics skill.**
+
+This is not optional. Literature reviews without visual elements are incomplete. Before finalizing any document:
+1. Generate at minimum ONE schematic or diagram (e.g., PRISMA flow diagram for systematic reviews)
+2. Prefer 2-3 figures for comprehensive reviews (search strategy flowchart, thematic synthesis diagram, conceptual framework)
+
+**How to generate figures:**
+- Use the **scientific-schematics** skill to generate AI-powered publication-quality diagrams
+- Simply describe your desired diagram in natural language
+- Nano Banana Pro will automatically generate, review, and refine the schematic
+
+**How to generate schematics:**
+```bash
+python scripts/generate_schematic.py "your diagram description" -o figures/output.png
+```
+
+The AI will automatically:
+- Create publication-quality images with proper formatting
+- Review and refine through multiple iterations
+- Ensure accessibility (colorblind-friendly, high contrast)
+- Save outputs in the figures/ directory
+
+**When to add schematics:**
+- PRISMA flow diagrams for systematic reviews
+- Literature search strategy flowcharts
+- Thematic synthesis diagrams
+- Research gap visualization maps
+- Citation network diagrams
+- Conceptual framework illustrations
+- Any complex concept that benefits from visualization
+
+For detailed guidance on creating schematics, refer to the scientific-schematics skill documentation.
+
+---
+
+## Core Workflow
+
+Literature reviews follow a structured, multi-phase workflow:
+
+### Phase 1: Planning and Scoping
+
+1. **Define Research Question**: Use PICO framework (Population, Intervention, Comparison, Outcome) for clinical/biomedical reviews
+ - Example: "What is the efficacy of CRISPR-Cas9 (I) for treating sickle cell disease (P) compared to standard care (C)?"
+
+2. **Establish Scope and Objectives**:
+ - Define clear, specific research questions
+ - Determine review type (narrative, systematic, scoping, meta-analysis)
+ - Set boundaries (time period, geographic scope, study types)
+
+3. **Develop Search Strategy**:
+ - Identify 2-4 main concepts from research question
+ - List synonyms, abbreviations, and related terms for each concept
+ - Plan Boolean operators (AND, OR, NOT) to combine terms
+ - Select minimum 3 complementary databases
+
+4. **Set Inclusion/Exclusion Criteria**:
+ - Date range (e.g., last 10 years: 2015-2024)
+ - Language (typically English, or specify multilingual)
+ - Publication types (peer-reviewed, preprints, reviews)
+ - Study designs (RCTs, observational, in vitro, etc.)
+ - Document all criteria clearly
+
+### Phase 2: Systematic Literature Search
+
+1. **Multi-Database Search**:
+
+ Select databases appropriate for the domain:
+
+ **Biomedical & Life Sciences:**
+ - Use `gget` skill: `gget search pubmed "search terms"` for PubMed/PMC
+ - Use `gget` skill: `gget search biorxiv "search terms"` for preprints
+ - Use `bioservices` skill for ChEMBL, KEGG, UniProt, etc.
+
+ **General Scientific Literature:**
+ - Search arXiv via direct API (preprints in physics, math, CS, q-bio)
+ - Search Semantic Scholar via API (200M+ papers, cross-disciplinary)
+ - Use Google Scholar for comprehensive coverage (manual or careful scraping)
+
+ **Specialized Databases:**
+ - Use `gget alphafold` for protein structures
+ - Use `gget cosmic` for cancer genomics
+ - Use `datacommons-client` for demographic/statistical data
+ - Use specialized databases as appropriate for the domain
+
+2. **Document Search Parameters**:
+ ```markdown
+ ## Search Strategy
+
+ ### Database: PubMed
+ - **Date searched**: 2024-10-25
+ - **Date range**: 2015-01-01 to 2024-10-25
+ - **Search string**:
+ ```
+ ("CRISPR"[Title] OR "Cas9"[Title])
+ AND ("sickle cell"[MeSH] OR "SCD"[Title/Abstract])
+ AND 2015:2024[Publication Date]
+ ```
+ - **Results**: 247 articles
+ ```
+
+ Repeat for each database searched.
+
+3. **Export and Aggregate Results**:
+ - Export results in JSON format from each database
+ - Combine all results into a single file
+ - Use `scripts/search_databases.py` for post-processing:
+ ```bash
+ python search_databases.py combined_results.json \
+ --deduplicate \
+ --format markdown \
+ --output aggregated_results.md
+ ```
+
+### Phase 3: Screening and Selection
+
+1. **Deduplication**:
+ ```bash
+ python search_databases.py results.json --deduplicate --output unique_results.json
+ ```
+ - Removes duplicates by DOI (primary) or title (fallback)
+ - Document number of duplicates removed
+
+2. **Title Screening**:
+ - Review all titles against inclusion/exclusion criteria
+ - Exclude obviously irrelevant studies
+ - Document number excluded at this stage
+
+3. **Abstract Screening**:
+ - Read abstracts of remaining studies
+ - Apply inclusion/exclusion criteria rigorously
+ - Document reasons for exclusion
+
+4. **Full-Text Screening**:
+ - Obtain full texts of remaining studies
+ - Conduct detailed review against all criteria
+ - Document specific reasons for exclusion
+ - Record final number of included studies
+
+5. **Create PRISMA Flow Diagram**:
+ ```
+ Initial search: n = X
+ ├─ After deduplication: n = Y
+ ├─ After title screening: n = Z
+ ├─ After abstract screening: n = A
+ └─ Included in review: n = B
+ ```
+
+### Phase 4: Data Extraction and Quality Assessment
+
+1. **Extract Key Data** from each included study:
+ - Study metadata (authors, year, journal, DOI)
+ - Study design and methods
+ - Sample size and population characteristics
+ - Key findings and results
+ - Limitations noted by authors
+ - Funding sources and conflicts of interest
+
+2. **Assess Study Quality**:
+ - **For RCTs**: Use Cochrane Risk of Bias tool
+ - **For observational studies**: Use Newcastle-Ottawa Scale
+ - **For systematic reviews**: Use AMSTAR 2
+ - Rate each study: High, Moderate, Low, or Very Low quality
+ - Consider excluding very low-quality studies
+
+3. **Organize by Themes**:
+ - Identify 3-5 major themes across studies
+ - Group studies by theme (studies may appear in multiple themes)
+ - Note patterns, consensus, and controversies
+
+### Phase 5: Synthesis and Analysis
+
+1. **Create Review Document** from template:
+ ```bash
+ cp assets/review_template.md my_literature_review.md
+ ```
+
+2. **Write Thematic Synthesis** (NOT study-by-study summaries):
+ - Organize Results section by themes or research questions
+ - Synthesize findings across multiple studies within each theme
+ - Compare and contrast different approaches and results
+ - Identify consensus areas and points of controversy
+ - Highlight the strongest evidence
+
+ Example structure:
+ ```markdown
+ #### 3.3.1 Theme: CRISPR Delivery Methods
+
+ Multiple delivery approaches have been investigated for therapeutic
+ gene editing. Viral vectors (AAV) were used in 15 studies^1-15^ and
+ showed high transduction efficiency (65-85%) but raised immunogenicity
+ concerns^3,7,12^. In contrast, lipid nanoparticles demonstrated lower
+ efficiency (40-60%) but improved safety profiles^16-23^.
+ ```
+
+3. **Critical Analysis**:
+ - Evaluate methodological strengths and limitations across studies
+ - Assess quality and consistency of evidence
+ - Identify knowledge gaps and methodological gaps
+ - Note areas requiring future research
+
+4. **Write Discussion**:
+ - Interpret findings in broader context
+ - Discuss clinical, practical, or research implications
+ - Acknowledge limitations of the review itself
+ - Compare with previous reviews if applicable
+ - Propose specific future research directions
+
+### Phase 6: Citation Verification
+
+**CRITICAL**: All citations must be verified for accuracy before final submission.
+
+1. **Verify All DOIs**:
+ ```bash
+ python scripts/verify_citations.py my_literature_review.md
+ ```
+
+ This script:
+ - Extracts all DOIs from the document
+ - Verifies each DOI resolves correctly
+ - Retrieves metadata from CrossRef
+ - Generates verification report
+ - Outputs properly formatted citations
+
+2. **Review Verification Report**:
+ - Check for any failed DOIs
+ - Verify author names, titles, and publication details match
+ - Correct any errors in the original document
+ - Re-run verification until all citations pass
+
+3. **Format Citations Consistently**:
+ - Choose one citation style and use throughout (see `references/citation_styles.md`)
+ - Common styles: APA, Nature, Vancouver, Chicago, IEEE
+ - Use verification script output to format citations correctly
+ - Ensure in-text citations match reference list format
+
+### Phase 7: Document Generation
+
+1. **Generate PDF**:
+ ```bash
+ python scripts/generate_pdf.py my_literature_review.md \
+ --citation-style apa \
+ --output my_review.pdf
+ ```
+
+ Options:
+ - `--citation-style`: apa, nature, chicago, vancouver, ieee
+ - `--no-toc`: Disable table of contents
+ - `--no-numbers`: Disable section numbering
+ - `--check-deps`: Check if pandoc/xelatex are installed
+
+2. **Review Final Output**:
+ - Check PDF formatting and layout
+ - Verify all sections are present
+ - Ensure citations render correctly
+ - Check that figures/tables appear properly
+ - Verify table of contents is accurate
+
+3. **Quality Checklist**:
+ - [ ] All DOIs verified with verify_citations.py
+ - [ ] Citations formatted consistently
+ - [ ] PRISMA flow diagram included (for systematic reviews)
+ - [ ] Search methodology fully documented
+ - [ ] Inclusion/exclusion criteria clearly stated
+ - [ ] Results organized thematically (not study-by-study)
+ - [ ] Quality assessment completed
+ - [ ] Limitations acknowledged
+ - [ ] References complete and accurate
+ - [ ] PDF generates without errors
+
+## Database-Specific Search Guidance
+
+### PubMed / PubMed Central
+
+Access via `gget` skill:
+```bash
+# Search PubMed
+gget search pubmed "CRISPR gene editing" -l 100
+
+# Search with filters
+# Use PubMed Advanced Search Builder to construct complex queries
+# Then execute via gget or direct Entrez API
+```
+
+**Search tips**:
+- Use MeSH terms: `"sickle cell disease"[MeSH]`
+- Field tags: `[Title]`, `[Title/Abstract]`, `[Author]`
+- Date filters: `2020:2024[Publication Date]`
+- Boolean operators: AND, OR, NOT
+- See MeSH browser: https://meshb.nlm.nih.gov/search
+
+### bioRxiv / medRxiv
+
+Access via `gget` skill:
+```bash
+gget search biorxiv "CRISPR sickle cell" -l 50
+```
+
+**Important considerations**:
+- Preprints are not peer-reviewed
+- Verify findings with caution
+- Check if preprint has been published (CrossRef)
+- Note preprint version and date
+
+### arXiv
+
+Access via direct API or WebFetch:
+```python
+# Example search categories:
+# q-bio.QM (Quantitative Methods)
+# q-bio.GN (Genomics)
+# q-bio.MN (Molecular Networks)
+# cs.LG (Machine Learning)
+# stat.ML (Machine Learning Statistics)
+
+# Search format: category AND terms
+search_query = "cat:q-bio.QM AND ti:\"single cell sequencing\""
+```
+
+### Semantic Scholar
+
+Access via direct API (requires API key, or use free tier):
+- 200M+ papers across all fields
+- Excellent for cross-disciplinary searches
+- Provides citation graphs and paper recommendations
+- Use for finding highly influential papers
+
+### Specialized Biomedical Databases
+
+Use appropriate skills:
+- **ChEMBL**: `bioservices` skill for chemical bioactivity
+- **UniProt**: `gget` or `bioservices` skill for protein information
+- **KEGG**: `bioservices` skill for pathways and genes
+- **COSMIC**: `gget` skill for cancer mutations
+- **AlphaFold**: `gget alphafold` for protein structures
+- **PDB**: `gget` or direct API for experimental structures
+
+### Citation Chaining
+
+Expand search via citation networks:
+
+1. **Forward citations** (papers citing key papers):
+ - Use Google Scholar "Cited by"
+ - Use Semantic Scholar or OpenAlex APIs
+ - Identifies newer research building on seminal work
+
+2. **Backward citations** (references from key papers):
+ - Extract references from included papers
+ - Identify highly cited foundational work
+ - Find papers cited by multiple included studies
+
+## Citation Style Guide
+
+Detailed formatting guidelines are in `references/citation_styles.md`. Quick reference:
+
+### APA (7th Edition)
+- In-text: (Smith et al., 2023)
+- Reference: Smith, J. D., Johnson, M. L., & Williams, K. R. (2023). Title. *Journal*, *22*(4), 301-318. https://doi.org/10.xxx/yyy
+
+### Nature
+- In-text: Superscript numbers^1,2^
+- Reference: Smith, J. D., Johnson, M. L. & Williams, K. R. Title. *Nat. Rev. Drug Discov.* **22**, 301-318 (2023).
+
+### Vancouver
+- In-text: Superscript numbers^1,2^
+- Reference: Smith JD, Johnson ML, Williams KR. Title. Nat Rev Drug Discov. 2023;22(4):301-18.
+
+**Always verify citations** with verify_citations.py before finalizing.
+
+## Best Practices
+
+### Search Strategy
+1. **Use multiple databases** (minimum 3): Ensures comprehensive coverage
+2. **Include preprint servers**: Captures latest unpublished findings
+3. **Document everything**: Search strings, dates, result counts for reproducibility
+4. **Test and refine**: Run pilot searches, review results, adjust search terms
+
+### Screening and Selection
+1. **Use clear criteria**: Document inclusion/exclusion criteria before screening
+2. **Screen systematically**: Title → Abstract → Full text
+3. **Document exclusions**: Record reasons for excluding studies
+4. **Consider dual screening**: For systematic reviews, have two reviewers screen independently
+
+### Synthesis
+1. **Organize thematically**: Group by themes, NOT by individual studies
+2. **Synthesize across studies**: Compare, contrast, identify patterns
+3. **Be critical**: Evaluate quality and consistency of evidence
+4. **Identify gaps**: Note what's missing or understudied
+
+### Quality and Reproducibility
+1. **Assess study quality**: Use appropriate quality assessment tools
+2. **Verify all citations**: Run verify_citations.py script
+3. **Document methodology**: Provide enough detail for others to reproduce
+4. **Follow guidelines**: Use PRISMA for systematic reviews
+
+### Writing
+1. **Be objective**: Present evidence fairly, acknowledge limitations
+2. **Be systematic**: Follow structured template
+3. **Be specific**: Include numbers, statistics, effect sizes where available
+4. **Be clear**: Use clear headings, logical flow, thematic organization
+
+## Common Pitfalls to Avoid
+
+1. **Single database search**: Misses relevant papers; always search multiple databases
+2. **No search documentation**: Makes review irreproducible; document all searches
+3. **Study-by-study summary**: Lacks synthesis; organize thematically instead
+4. **Unverified citations**: Leads to errors; always run verify_citations.py
+5. **Too broad search**: Yields thousands of irrelevant results; refine with specific terms
+6. **Too narrow search**: Misses relevant papers; include synonyms and related terms
+7. **Ignoring preprints**: Misses latest findings; include bioRxiv, medRxiv, arXiv
+8. **No quality assessment**: Treats all evidence equally; assess and report quality
+9. **Publication bias**: Only positive results published; note potential bias
+10. **Outdated search**: Field evolves rapidly; clearly state search date
+
+## Example Workflow
+
+Complete workflow for a biomedical literature review:
+
+```bash
+# 1. Create review document from template
+cp assets/review_template.md crispr_sickle_cell_review.md
+
+# 2. Search multiple databases using appropriate skills
+# - Use gget skill for PubMed, bioRxiv
+# - Use direct API access for arXiv, Semantic Scholar
+# - Export results in JSON format
+
+# 3. Aggregate and process results
+python scripts/search_databases.py combined_results.json \
+ --deduplicate \
+ --rank citations \
+ --year-start 2015 \
+ --year-end 2024 \
+ --format markdown \
+ --output search_results.md \
+ --summary
+
+# 4. Screen results and extract data
+# - Manually screen titles, abstracts, full texts
+# - Extract key data into the review document
+# - Organize by themes
+
+# 5. Write the review following template structure
+# - Introduction with clear objectives
+# - Detailed methodology section
+# - Results organized thematically
+# - Critical discussion
+# - Clear conclusions
+
+# 6. Verify all citations
+python scripts/verify_citations.py crispr_sickle_cell_review.md
+
+# Review the citation report
+cat crispr_sickle_cell_review_citation_report.json
+
+# Fix any failed citations and re-verify
+python scripts/verify_citations.py crispr_sickle_cell_review.md
+
+# 7. Generate professional PDF
+python scripts/generate_pdf.py crispr_sickle_cell_review.md \
+ --citation-style nature \
+ --output crispr_sickle_cell_review.pdf
+
+# 8. Review final PDF and markdown outputs
+```
+
+## Integration with Other Skills
+
+This skill works seamlessly with other scientific skills:
+
+### Database Access Skills
+- **gget**: PubMed, bioRxiv, COSMIC, AlphaFold, Ensembl, UniProt
+- **bioservices**: ChEMBL, KEGG, Reactome, UniProt, PubChem
+- **datacommons-client**: Demographics, economics, health statistics
+
+### Analysis Skills
+- **pydeseq2**: RNA-seq differential expression (for methods sections)
+- **scanpy**: Single-cell analysis (for methods sections)
+- **anndata**: Single-cell data (for methods sections)
+- **biopython**: Sequence analysis (for background sections)
+
+### Visualization Skills
+- **matplotlib**: Generate figures and plots for review
+- **seaborn**: Statistical visualizations
+
+### Writing Skills
+- **brand-guidelines**: Apply institutional branding to PDF
+- **internal-comms**: Adapt review for different audiences
+
+## Resources
+
+### Bundled Resources
+
+**Scripts:**
+- `scripts/verify_citations.py`: Verify DOIs and generate formatted citations
+- `scripts/generate_pdf.py`: Convert markdown to professional PDF
+- `scripts/search_databases.py`: Process, deduplicate, and format search results
+
+**References:**
+- `references/citation_styles.md`: Detailed citation formatting guide (APA, Nature, Vancouver, Chicago, IEEE)
+- `references/database_strategies.md`: Comprehensive database search strategies
+
+**Assets:**
+- `assets/review_template.md`: Complete literature review template with all sections
+
+### External Resources
+
+**Guidelines:**
+- PRISMA (Systematic Reviews): http://www.prisma-statement.org/
+- Cochrane Handbook: https://training.cochrane.org/handbook
+- AMSTAR 2 (Review Quality): https://amstar.ca/
+
+**Tools:**
+- MeSH Browser: https://meshb.nlm.nih.gov/search
+- PubMed Advanced Search: https://pubmed.ncbi.nlm.nih.gov/advanced/
+- Boolean Search Guide: https://www.ncbi.nlm.nih.gov/books/NBK3827/
+
+**Citation Styles:**
+- APA Style: https://apastyle.apa.org/
+- Nature Portfolio: https://www.nature.com/nature-portfolio/editorial-policies/reporting-standards
+- NLM/Vancouver: https://www.nlm.nih.gov/bsd/uniform_requirements.html
+
+## Dependencies
+
+### Required Python Packages
+```bash
+pip install requests # For citation verification
+```
+
+### Required System Tools
+```bash
+# For PDF generation
+brew install pandoc # macOS
+apt-get install pandoc # Linux
+
+# For LaTeX (PDF generation)
+brew install --cask mactex # macOS
+apt-get install texlive-xetex # Linux
+```
+
+Check dependencies:
+```bash
+python scripts/generate_pdf.py --check-deps
+```
+
+## Summary
+
+This literature-review skill provides:
+
+1. **Systematic methodology** following academic best practices
+2. **Multi-database integration** via existing scientific skills
+3. **Citation verification** ensuring accuracy and credibility
+4. **Professional output** in markdown and PDF formats
+5. **Comprehensive guidance** covering the entire review process
+6. **Quality assurance** with verification and validation tools
+7. **Reproducibility** through detailed documentation requirements
+
+Conduct thorough, rigorous literature reviews that meet academic standards and provide comprehensive synthesis of current knowledge in any domain.
diff --git a/scientific-skills/literature-review/assets/review_template.md b/scientific-skills/literature-review/assets/review_template.md
new file mode 100644
index 0000000..601325b
--- /dev/null
+++ b/scientific-skills/literature-review/assets/review_template.md
@@ -0,0 +1,412 @@
+# [Literature Review Title]
+
+**Authors**: [Author Names and Affiliations]
+**Date**: [Date]
+**Review Type**: [Narrative / Systematic / Scoping / Meta-Analysis / Umbrella Review]
+**Review Protocol**: [PROSPERO ID if registered, or state "Not registered"]
+**PRISMA Compliance**: [Yes/No/Partial - specify which guidelines]
+
+---
+
+## Abstract
+
+**Background**: [Context and rationale]
+**Objectives**: [Primary and secondary objectives]
+**Methods**: [Databases, dates, selection criteria, quality assessment]
+**Results**: [n studies included; key findings by theme]
+**Conclusions**: [Main conclusions and implications]
+**Registration**: [PROSPERO ID or "Not registered"]
+**Keywords**: [5-8 keywords]
+
+---
+
+## 1. Introduction
+
+### 1.1 Background and Context
+
+[Provide background information on the topic. Establish why this literature review is important and timely. Discuss the broader context and current state of knowledge.]
+
+### 1.2 Scope and Objectives
+
+[Clearly define the scope of the review and state the specific objectives. What questions will this review address?]
+
+**Primary Research Questions:**
+1. [Research question 1]
+2. [Research question 2]
+3. [Research question 3]
+
+### 1.3 Significance
+
+[Explain the significance of this review. Why is it important to synthesize this literature now? What gaps does it fill?]
+
+---
+
+## 2. Methodology
+
+### 2.1 Protocol and Registration
+
+**Protocol**: [PROSPERO ID / OSF link / Not registered]
+**Deviations**: [Document any protocol deviations]
+**PRISMA**: [Checklist in Appendix B]
+
+### 2.2 Search Strategy
+
+**Databases:** [PubMed, Scopus, Web of Science, bioRxiv, etc.]
+**Supplementary:** [Citation chaining, grey literature, trial registries]
+
+**Search String Example:**
+```
+("CRISPR"[Title/Abstract] OR "Cas9"[Title/Abstract]) AND
+("disease"[MeSH Terms]) AND ("2015/01/01"[Date] : "2024/12/31"[Date])
+```
+
+**Dates:** [YYYY-MM-DD to YYYY-MM-DD] | **Executed:** [Date]
+**Validation:** [Key papers used to test search strategy]
+
+### 2.3 Tools and Software
+
+**Screening:** [Rayyan, Covidence, ASReview]
+**Analysis:** [VOSviewer, R, Python]
+**Citation Management:** [Zotero, Mendeley, EndNote]
+**AI Tools:** [Any AI-assisted tools used; document validation approach]
+
+### 2.4 Inclusion and Exclusion Criteria
+
+**Inclusion Criteria:**
+- [Criterion 1: e.g., Published between 2015-2024]
+- [Criterion 2: e.g., Peer-reviewed articles and preprints]
+- [Criterion 3: e.g., English language]
+- [Criterion 4: e.g., Human or animal studies]
+- [Criterion 5: e.g., Original research or systematic reviews]
+
+**Exclusion Criteria:**
+- [Criterion 1: e.g., Case reports with n<5]
+- [Criterion 2: e.g., Conference abstracts without full text]
+- [Criterion 3: e.g., Editorials and commentaries]
+- [Criterion 4: e.g., Duplicate publications]
+- [Criterion 5: e.g., Retracted articles]
+- [Criterion 6: e.g., Studies with unavailable full text after author contact]
+
+### 2.5 Study Selection
+
+**Reviewers:** [n independent reviewers] | **Conflict resolution:** [Method]
+**Inter-rater reliability:** [Cohen's kappa = X]
+
+**PRISMA Flow:**
+```
+Records identified: n=[X] → Deduplicated: n=[Y] →
+Title/abstract screened: n=[Y] → Full-text assessed: n=[Z] → Included: n=[N]
+```
+
+**Exclusion reasons:** [List with counts]
+
+### 2.6 Data Extraction
+
+**Method:** [Standardized form (Appendix E); pilot-tested on n studies]
+**Extractors:** [n independent] | **Verification:** [Double-checked]
+
+**Items:** Study ID, design, population, interventions/exposures, outcomes, statistics, funding, COI, bias domains
+
+**Missing data:** [Author contact protocol]
+
+### 2.7 Quality Assessment
+
+**Tool:** [Cochrane RoB 2.0 / ROBINS-I / Newcastle-Ottawa / AMSTAR 2 / JBI]
+**Method:** [2 independent reviewers; third for conflicts]
+**Rating:** [Low/Moderate/High risk of bias]
+**Publication bias:** [Funnel plots, Egger's test - if meta-analysis]
+
+### 2.8 Synthesis and Analysis
+
+**Approach:** [Narrative / Meta-analysis / Both]
+**Statistics** (if meta-analysis): Effect measures, heterogeneity (I², τ²), sensitivity analyses, subgroups
+**Software:** [RevMan, R, Stata]
+**Certainty:** [GRADE framework; factors: bias, inconsistency, indirectness, imprecision]
+
+---
+
+## 3. Results
+
+### 3.1 Study Selection
+
+**Summary:** [X records → Y deduplicated → Z full-text → N included (M in meta-analysis)]
+**Study types:** [RCTs: n=X, Observational: n=Y, Reviews: n=Z]
+**Years:** [Range; peak year]
+**Geography:** [Countries represented]
+**Source:** [Peer-reviewed: n=X, Preprints: n=Y]
+
+### 3.2 Bibliometric Overview
+
+[Optional: Trends, journal distribution, author networks, citations, keywords - if analyzed with VOSviewer or similar]
+
+### 3.3 Study Characteristics
+
+| Study | Year | Design | Sample Size | Key Methods | Main Findings | Quality |
+|-------|------|--------|-------------|-------------|---------------|---------|
+| First Author et al. | 2023 | [Type] | n=[X] | [Methods] | [Brief findings] | [Low/Mod/High RoB] |
+
+**Quality:** Low RoB: n=X ([%]); Moderate: n=Y ([%]); High: n=Z ([%])
+
+### 3.4 Thematic Synthesis
+
+[Organize by themes, NOT study-by-study. Synthesize across studies to identify consensus, controversies, and gaps.]
+
+#### 3.4.1 Theme 1: [Title]
+
+**Findings:** [Synthesis of key findings from multiple studies]
+**Supporting studies:** [X, Y, Z]
+**Contradictory evidence:** [If any]
+**Certainty:** [GRADE rating if applicable]
+
+### 3.5 Methodological Approaches
+
+**Common methods:** [Method 1 (n studies), Method 2 (n studies)]
+**Emerging techniques:** [New approaches observed]
+**Methodological quality:** [Overall assessment]
+
+### 3.6 Meta-Analysis Results
+
+[Include only if conducting meta-analysis]
+
+**Effect estimates:** [Primary/secondary outcomes with 95% CI, p-values]
+**Heterogeneity:** [I²=X%, τ²=Y, interpretation]
+**Subgroups & sensitivity:** [Key findings from analyses]
+**Publication bias:** [Funnel plot, Egger's p=X]
+**Forest plots:** [Include for primary outcomes]
+
+### 3.7 Knowledge Gaps
+
+**Knowledge:** [Unanswered research questions]
+**Methodological:** [Study design/measurement issues]
+**Translational:** [Research-to-practice gaps]
+**Populations:** [Underrepresented groups/contexts]
+
+---
+
+## 4. Discussion
+
+### 4.1 Main Findings
+
+[Synthesize key findings by research question]
+
+**Principal findings:** [Top 3-5 takeaways]
+**Consensus:** [Where studies agree]
+**Controversy:** [Conflicting results]
+
+### 4.2 Interpretation and Implications
+
+**Context:** [How findings advance/challenge current understanding]
+**Mechanisms:** [Potential explanations for observed patterns]
+
+**Implications for:**
+- **Practice:** [Actionable recommendations]
+- **Policy:** [If relevant]
+- **Research:** [Theoretical, methodological, priority directions]
+
+### 4.3 Strengths and Limitations
+
+**Strengths:** [Comprehensive search, rigorous methods, large evidence base, transparency]
+
+**Limitations:**
+- Search/selection: [Language bias, database coverage, grey literature, publication bias]
+- Methodological: [Heterogeneity, study quality]
+- Temporal: [Rapid evolution, search cutoff date]
+
+**Impact:** [How limitations affect conclusions]
+
+### 4.4 Comparison with Previous Reviews
+
+[If relevant: How does this review update/differ from prior reviews?]
+
+### 4.5 Future Research
+
+**Priority questions:**
+1. [Question] - Rationale, suggested approach, expected impact
+2. [Question] - Rationale, suggested approach, expected impact
+3. [Question] - Rationale, suggested approach, expected impact
+
+**Recommendations:** [Methodological improvements, understudied populations, emerging technologies]
+
+---
+
+## 5. Conclusions
+
+[Concise conclusions addressing research questions]
+
+1. [Conclusion directly addressing primary research question]
+2. [Key finding conclusion]
+3. [Gap/future direction conclusion]
+
+**Evidence certainty:** [High/Moderate/Low/Very Low]
+**Translation readiness:** [Ready / Needs more research / Preliminary]
+
+---
+
+## 6. Declarations
+
+### Author Contributions
+[CRediT taxonomy: Author 1 - Conceptualization, Methodology, Writing; Author 2 - Analysis, Review; etc.]
+
+### Funding
+[Grant details with numbers] OR [No funding received]
+
+### Conflicts of Interest
+[Author-specific declarations] OR [None]
+
+### Data Availability
+**Protocol:** [PROSPERO/OSF ID or "Not registered"]
+**Data/Code:** [Repository URL/DOI or "Available upon request"]
+**Materials:** [Search strategies (Appendix A), PRISMA checklist (Appendix B), extraction form (Appendix E)]
+
+### Acknowledgments
+[Contributors not meeting authorship criteria, librarians, patient involvement]
+
+---
+
+## 7. References
+
+[Use consistent style: APA / Nature / Vancouver]
+
+**Format examples:**
+
+APA: Author, A. A., & Author, B. B. (Year). Title. *Journal*, *volume*(issue), pages. https://doi.org/xx.xxxx
+
+Nature: Author, A. A. & Author, B. B. Title. *J. Name* **volume**, pages (year).
+
+Vancouver: Author AA, Author BB. Title. J Abbrev. Year;volume(issue):pages. doi:xx.xxxx
+
+1. [First reference]
+2. [Second reference]
+3. [Continue...]
+
+---
+
+## 8. Appendices
+
+### Appendix A: Search Strings
+
+**PubMed** (Date: YYYY-MM-DD; Results: n)
+```
+[Complete search string with operators and MeSH terms]
+```
+
+[Repeat for each database: Scopus, Web of Science, bioRxiv, etc.]
+
+### Appendix B: PRISMA Checklist
+
+| Section | Item | Reported? | Page |
+|---------|------|-----------|------|
+| Title | Identify as systematic review | Yes/No | # |
+| Abstract | Structured summary | Yes/No | # |
+| Methods | Eligibility, sources, search, selection, data, quality | Yes/No | # |
+| Results | Selection, characteristics, risk of bias, syntheses | Yes/No | # |
+| Discussion | Interpretation, limitations, conclusions | Yes/No | # |
+| Other | Registration, support, conflicts, availability | Yes/No | # |
+
+### Appendix C: Excluded Studies
+
+| Study | Year | Reason | Category |
+|-------|------|--------|----------|
+| Author et al. | Year | [Reason] | [Wrong population/outcome/design/etc.] |
+
+**Summary:** Wrong population (n=X), Wrong outcome (n=Y), etc.
+
+### Appendix D: Quality Assessment
+
+**Tool:** [Cochrane RoB 2.0 / ROBINS-I / Newcastle-Ottawa / etc.]
+
+| Study | Domain 1 | Domain 2 | Domain 3 | Overall |
+|-------|----------|----------|----------|---------|
+| Study 1 | Low | Low | Some concerns | Low |
+| Study 2 | [Score] | [Score] | [Score] | [Overall] |
+
+### Appendix E: Data Extraction Form
+
+```
+STUDY: Author______ Year______ DOI______
+DESIGN: □RCT □Cohort □Case-Control □Cross-sectional □Other______
+POPULATION: n=_____ Age_____ Setting_____
+INTERVENTION/EXPOSURE: _____
+OUTCOMES: Primary_____ Secondary_____
+RESULTS: Effect size_____ 95%CI_____ p=_____
+QUALITY: □Low □Moderate □High RoB
+FUNDING/COI: _____
+```
+
+### Appendix F: Meta-Analysis Details
+
+[Only if meta-analysis performed]
+
+**Software:** [R 4.x.x with meta/metafor packages / RevMan / Stata]
+**Model:** [Random-effects; justification]
+**Code:** [Link to repository]
+**Sensitivity analyses:** [Details]
+
+### Appendix G: Author Contacts
+
+| Study | Contact Date | Response | Data Received |
+|-------|--------------|----------|---------------|
+| Author et al. | YYYY-MM-DD | Yes/No | Yes/No/Partial |
+
+---
+
+## 9. Supplementary Materials
+
+[If applicable]
+
+**Tables:** S1 (Full study characteristics), S2 (Quality scores), S3 (Subgroups), S4 (Sensitivity)
+**Figures:** S1 (PRISMA diagram), S2 (Risk of bias), S3 (Funnel plot), S4 (Forest plots), S5 (Networks)
+**Data:** S1 (Extraction file), S2 (Search results), S3 (Analysis code), S4 (PRISMA checklist)
+**Repository:** [OSF/GitHub/Zenodo URL with DOI]
+
+---
+
+## Review Metadata
+
+**Registration:** [Registry] ID: [Number] (Date: YYYY-MM-DD)
+**Search dates:** Initial: [Date]; Updated: [Date]
+**Version:** [1.0] | **Last updated:** [Date]
+
+**Quality checks:**
+- [ ] Citations verified with verify_citations.py
+- [ ] PRISMA checklist completed
+- [ ] Search reproducible
+- [ ] Independent data verification
+- [ ] Code peer-reviewed
+- [ ] All authors approved
+
+---
+
+## Usage Notes
+
+**Review type adaptations:**
+- Systematic Review: Use all sections
+- Meta-Analysis: Include sections 3.6, Appendix F
+- Narrative Review: May omit some methodology detail
+- Scoping Review: Follow PRISMA-ScR, may omit quality assessment
+
+**Key principles:**
+1. Remove all [bracketed placeholders]
+2. Follow PRISMA 2020 guidelines
+3. Pre-register when feasible (PROSPERO/OSF)
+4. Use thematic synthesis, not study-by-study
+5. Be transparent and reproducible
+6. Verify all DOIs before submission
+7. Make data/code openly available
+
+**Common pitfalls to avoid:**
+- Don't list studies - synthesize them
+- Don't cherry-pick results
+- Don't ignore limitations
+- Don't overstate conclusions
+- Don't skip publication bias assessment
+
+**Resources:**
+- PRISMA 2020: http://prisma-statement.org/
+- PROSPERO: https://www.crd.york.ac.uk/prospero/
+- Cochrane Handbook: https://training.cochrane.org/handbook
+- GRADE: https://www.gradeworkinggroup.org/
+
+**DELETE THIS SECTION FROM YOUR FINAL REVIEW**
+
+---
diff --git a/scientific-skills/literature-review/references/citation_styles.md b/scientific-skills/literature-review/references/citation_styles.md
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+++ b/scientific-skills/literature-review/references/citation_styles.md
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+# Citation Styles Reference
+
+This document provides detailed guidelines for formatting citations in various academic styles commonly used in literature reviews.
+
+## APA Style (7th Edition)
+
+### Journal Articles
+
+**Format**: Author, A. A., Author, B. B., & Author, C. C. (Year). Title of article. *Title of Periodical*, *volume*(issue), page range. https://doi.org/xx.xxx/yyyy
+
+**Example**: Smith, J. D., Johnson, M. L., & Williams, K. R. (2023). Machine learning approaches in drug discovery. *Nature Reviews Drug Discovery*, *22*(4), 301-318. https://doi.org/10.1038/nrd.2023.001
+
+### Books
+
+**Format**: Author, A. A. (Year). *Title of work: Capital letter also for subtitle*. Publisher Name. https://doi.org/xxxx
+
+**Example**: Kumar, V., Abbas, A. K., & Aster, J. C. (2021). *Robbins and Cotran pathologic basis of disease* (10th ed.). Elsevier.
+
+### Book Chapters
+
+**Format**: Author, A. A., & Author, B. B. (Year). Title of chapter. In E. E. Editor & F. F. Editor (Eds.), *Title of book* (pp. xx-xx). Publisher.
+
+**Example**: Brown, P. O., & Botstein, D. (2020). Exploring the new world of the genome with DNA microarrays. In M. B. Eisen & P. O. Brown (Eds.), *DNA microarrays: A molecular cloning manual* (pp. 1-45). Cold Spring Harbor Laboratory Press.
+
+### Preprints
+
+**Format**: Author, A. A., & Author, B. B. (Year). Title of preprint. *Repository Name*. https://doi.org/xxxx
+
+**Example**: Zhang, Y., Chen, L., & Wang, H. (2024). Novel therapeutic targets in Alzheimer's disease. *bioRxiv*. https://doi.org/10.1101/2024.01.001
+
+### Conference Papers
+
+**Format**: Author, A. A. (Year, Month day-day). Title of paper. In E. E. Editor (Ed.), *Title of conference proceedings* (pp. xx-xx). Publisher. https://doi.org/xxxx
+
+---
+
+## Nature Style
+
+### Journal Articles
+
+**Format**: Author, A. A., Author, B. B. & Author, C. C. Title of article. *J. Name* **volume**, page range (year).
+
+**Example**: Smith, J. D., Johnson, M. L. & Williams, K. R. Machine learning approaches in drug discovery. *Nat. Rev. Drug Discov.* **22**, 301-318 (2023).
+
+### Books
+
+**Format**: Author, A. A. & Author, B. B. *Book Title* (Publisher, Year).
+
+**Example**: Kumar, V., Abbas, A. K. & Aster, J. C. *Robbins and Cotran Pathologic Basis of Disease* 10th edn (Elsevier, 2021).
+
+### Multiple Authors
+
+- 1-2 authors: List all
+- 3+ authors: List first author followed by "et al."
+
+**Example**: Zhang, Y. et al. Novel therapeutic targets in Alzheimer's disease. *bioRxiv* https://doi.org/10.1101/2024.01.001 (2024).
+
+---
+
+## Chicago Style (Author-Date)
+
+### Journal Articles
+
+**Format**: Author, First Name Middle Initial. Year. "Article Title." *Journal Title* volume, no. issue (Month): page range. https://doi.org/xxxx.
+
+**Example**: Smith, John D., Mary L. Johnson, and Karen R. Williams. 2023. "Machine Learning Approaches in Drug Discovery." *Nature Reviews Drug Discovery* 22, no. 4 (April): 301-318. https://doi.org/10.1038/nrd.2023.001.
+
+### Books
+
+**Format**: Author, First Name Middle Initial. Year. *Book Title: Subtitle*. Edition. Place: Publisher.
+
+**Example**: Kumar, Vinay, Abul K. Abbas, and Jon C. Aster. 2021. *Robbins and Cotran Pathologic Basis of Disease*. 10th ed. Philadelphia: Elsevier.
+
+---
+
+## Vancouver Style (Numbered)
+
+### Journal Articles
+
+**Format**: Author AA, Author BB, Author CC. Title of article. Abbreviated Journal Name. Year;volume(issue):page range.
+
+**Example**: Smith JD, Johnson ML, Williams KR. Machine learning approaches in drug discovery. Nat Rev Drug Discov. 2023;22(4):301-18.
+
+### Books
+
+**Format**: Author AA, Author BB. Title of book. Edition. Place: Publisher; Year.
+
+**Example**: Kumar V, Abbas AK, Aster JC. Robbins and Cotran pathologic basis of disease. 10th ed. Philadelphia: Elsevier; 2021.
+
+### Citation in Text
+
+Use superscript numbers in order of appearance: "Recent studies^1,2^ have shown..."
+
+---
+
+## IEEE Style
+
+### Journal Articles
+
+**Format**: [#] A. A. Author, B. B. Author, and C. C. Author, "Title of article," *Abbreviated Journal Name*, vol. x, no. x, pp. xxx-xxx, Month Year.
+
+**Example**: [1] J. D. Smith, M. L. Johnson, and K. R. Williams, "Machine learning approaches in drug discovery," *Nat. Rev. Drug Discov.*, vol. 22, no. 4, pp. 301-318, Apr. 2023.
+
+### Books
+
+**Format**: [#] A. A. Author, *Title of Book*, xth ed. City, State: Publisher, Year.
+
+**Example**: [2] V. Kumar, A. K. Abbas, and J. C. Aster, *Robbins and Cotran Pathologic Basis of Disease*, 10th ed. Philadelphia, PA: Elsevier, 2021.
+
+---
+
+## Common Abbreviations for Journal Names
+
+- Nature: Nat.
+- Science: Science
+- Cell: Cell
+- Nature Reviews Drug Discovery: Nat. Rev. Drug Discov.
+- Journal of the American Chemical Society: J. Am. Chem. Soc.
+- Proceedings of the National Academy of Sciences: Proc. Natl. Acad. Sci. U.S.A.
+- PLOS ONE: PLoS ONE
+- Bioinformatics: Bioinformatics
+- Nucleic Acids Research: Nucleic Acids Res.
+
+---
+
+## DOI Best Practices
+
+1. **Always verify DOIs**: Use the verify_citations.py script to check all DOIs
+2. **Format as URLs**: https://doi.org/10.xxxx/yyyy (preferred over doi:10.xxxx/yyyy)
+3. **No period after DOI**: DOI should be the last element without trailing punctuation
+4. **Resolve redirects**: Check that DOIs resolve to the correct article
+
+---
+
+## In-Text Citation Guidelines
+
+### APA Style
+- (Smith et al., 2023)
+- Smith et al. (2023) demonstrated...
+- Multiple citations: (Brown, 2022; Smith et al., 2023; Zhang, 2024)
+
+### Nature Style
+- Superscript numbers: Recent studies^1,2^ have shown...
+- Or: Recent studies (refs 1,2) have shown...
+
+### Chicago Style
+- (Smith, Johnson, and Williams 2023)
+- Smith, Johnson, and Williams (2023) found...
+
+---
+
+## Reference List Organization
+
+### By Citation Style
+- **APA, Chicago**: Alphabetical by first author's last name
+- **Nature, Vancouver, IEEE**: Numerical order of first appearance in text
+
+### Hanging Indents
+Most styles use hanging indents where the first line is flush left and subsequent lines are indented.
+
+### Consistency
+Maintain consistent formatting throughout:
+- Capitalization (title case vs. sentence case)
+- Journal name abbreviations
+- DOI presentation
+- Author name format
diff --git a/scientific-skills/literature-review/references/database_strategies.md b/scientific-skills/literature-review/references/database_strategies.md
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+# Literature Database Search Strategies
+
+This document provides comprehensive guidance for searching multiple literature databases systematically and effectively.
+
+## Available Databases and Skills
+
+### Biomedical & Life Sciences
+
+#### PubMed / PubMed Central
+- **Access**: Use `gget` skill or WebFetch tool
+- **Coverage**: 35M+ citations in biomedical literature
+- **Best for**: Clinical studies, biomedical research, genetics, molecular biology
+- **Search tips**: Use MeSH terms, Boolean operators (AND, OR, NOT), field tags [Title], [Author]
+- **Example**: `"CRISPR"[Title] AND "gene editing"[Title/Abstract] AND 2020:2024[Publication Date]`
+
+#### bioRxiv / medRxiv
+- **Access**: Use `gget` skill or direct API
+- **Coverage**: Preprints in biology and medicine
+- **Best for**: Latest unpublished research, cutting-edge findings
+- **Note**: Not peer-reviewed; verify findings with caution
+- **Search tips**: Search by category (bioinformatics, genomics, etc.)
+
+### General Scientific Literature
+
+#### arXiv
+- **Access**: Direct API access
+- **Coverage**: Preprints in physics, mathematics, computer science, quantitative biology
+- **Best for**: Computational methods, bioinformatics algorithms, theoretical work
+- **Categories**: q-bio (Quantitative Biology), cs.LG (Machine Learning), stat.ML (Statistics)
+- **Search format**: `cat:q-bio.QM AND title:"single cell"`
+
+#### Semantic Scholar
+- **Access**: Direct API (requires API key)
+- **Coverage**: 200M+ papers across all fields
+- **Best for**: Cross-disciplinary searches, citation graphs, paper recommendations
+- **Features**: Influential citations, paper summaries, related papers
+- **Rate limits**: 100 requests/5 minutes with API key
+
+#### Google Scholar
+- **Access**: Web scraping (use cautiously) or manual search
+- **Coverage**: Comprehensive across all fields
+- **Best for**: Finding highly cited papers, conference proceedings, theses
+- **Limitations**: No official API, rate limiting
+- **Export**: Use "Cite" feature for formatted citations
+
+### Specialized Databases
+
+#### ChEMBL / PubChem
+- **Access**: Use `gget` skill or `bioservices` skill
+- **Coverage**: Chemical compounds, bioactivity data, drug molecules
+- **Best for**: Drug discovery, chemical biology, medicinal chemistry
+- **ChEMBL**: 2M+ compounds, bioactivity data
+- **PubChem**: 110M+ compounds, assay data
+
+#### UniProt
+- **Access**: Use `gget` skill or `bioservices` skill
+- **Coverage**: Protein sequence and functional information
+- **Best for**: Protein research, sequence analysis, functional annotations
+- **Search by**: Protein name, gene name, organism, function
+
+#### KEGG (Kyoto Encyclopedia of Genes and Genomes)
+- **Access**: Use `bioservices` skill
+- **Coverage**: Pathways, diseases, drugs, genes
+- **Best for**: Pathway analysis, systems biology, metabolic research
+
+#### COSMIC (Catalogue of Somatic Mutations in Cancer)
+- **Access**: Use `gget` skill or direct download
+- **Coverage**: Cancer genomics, somatic mutations
+- **Best for**: Cancer research, mutation analysis
+
+#### AlphaFold Database
+- **Access**: Use `gget` skill with `alphafold` command
+- **Coverage**: 200M+ protein structure predictions
+- **Best for**: Structural biology, protein modeling
+
+#### PDB (Protein Data Bank)
+- **Access**: Use `gget` or direct API
+- **Coverage**: Experimental 3D structures of proteins, nucleic acids
+- **Best for**: Structural biology, drug design, molecular modeling
+
+### Citation & Reference Management
+
+#### OpenAlex
+- **Access**: Direct API (free, no key required)
+- **Coverage**: 250M+ works, comprehensive metadata
+- **Best for**: Citation analysis, author disambiguation, institutional research
+- **Features**: Open access, excellent for bibliometrics
+
+#### Dimensions
+- **Access**: Free tier available
+- **Coverage**: Publications, grants, patents, clinical trials
+- **Best for**: Research impact, funding analysis, translational research
+
+---
+
+## Search Strategy Framework
+
+### 1. Define Research Question (PICO Framework)
+
+For clinical/biomedical reviews:
+- **P**opulation: Who is the study about?
+- **I**ntervention: What is being tested?
+- **C**omparison: What is it compared to?
+- **O**utcome: What are the results?
+
+**Example**: "What is the efficacy of CRISPR-Cas9 gene therapy (I) for treating sickle cell disease (P) compared to standard care (C) in improving patient outcomes (O)?"
+
+### 2. Develop Search Terms
+
+#### Primary Concepts
+Identify 2-4 main concepts from your research question.
+
+**Example**:
+- Concept 1: CRISPR, Cas9, gene editing
+- Concept 2: sickle cell disease, SCD, hemoglobin disorders
+- Concept 3: gene therapy, therapeutic editing
+
+#### Synonyms & Related Terms
+List alternative terms, abbreviations, and related concepts.
+
+**Tool**: Use MeSH (Medical Subject Headings) browser for standardized terms
+
+#### Boolean Operators
+- **AND**: Narrows search (must include both terms)
+- **OR**: Broadens search (includes either term)
+- **NOT**: Excludes terms
+
+**Example**: `(CRISPR OR Cas9 OR "gene editing") AND ("sickle cell" OR SCD) AND therapy`
+
+#### Wildcards & Truncation
+- `*` or `%`: Matches any characters
+- `?`: Matches single character
+
+**Example**: `genom*` matches genomic, genomics, genome
+
+### 3. Set Inclusion/Exclusion Criteria
+
+#### Inclusion Criteria
+- **Date range**: e.g., 2015-2024 (last 10 years)
+- **Language**: English (or specify multilingual)
+- **Publication type**: Peer-reviewed articles, reviews, preprints
+- **Study design**: RCTs, cohort studies, meta-analyses
+- **Population**: Human, animal models, in vitro
+
+#### Exclusion Criteria
+- Case reports (n<5)
+- Conference abstracts without full text
+- Non-original research (editorials, commentaries)
+- Duplicate publications
+- Retracted articles
+
+### 4. Database Selection Strategy
+
+#### Multi-Database Approach
+Search at least 3 complementary databases:
+
+1. **Primary database**: PubMed (biomedical) or arXiv (computational)
+2. **Preprint server**: bioRxiv/medRxiv or arXiv
+3. **Comprehensive database**: Semantic Scholar or Google Scholar
+4. **Specialized database**: ChEMBL, UniProt, or field-specific
+
+#### Database-Specific Syntax
+
+| Database | Field Tags | Example |
+|----------|-----------|---------|
+| PubMed | [Title], [Author], [MeSH] | "CRISPR"[Title] AND 2020:2024[DP] |
+| arXiv | ti:, au:, cat: | ti:"machine learning" AND cat:q-bio.QM |
+| Semantic Scholar | title:, author:, year: | title:"deep learning" year:2020-2024 |
+
+---
+
+## Search Execution Workflow
+
+### Phase 1: Pilot Search
+1. Run initial search with broad terms
+2. Review first 50 results for relevance
+3. Note common keywords and MeSH terms
+4. Refine search strategy
+
+### Phase 2: Comprehensive Search
+1. Execute refined searches across all selected databases
+2. Export results in standard format (RIS, BibTeX, JSON)
+3. Document search strings and date for each database
+4. Record number of results per database
+
+### Phase 3: Deduplication
+1. Import all results into a single file
+2. Use `search_databases.py --deduplicate` to remove duplicates
+3. Identify duplicates by DOI (primary) or title (fallback)
+4. Keep the version with most complete metadata
+
+### Phase 4: Screening
+1. **Title screening**: Review titles, exclude obviously irrelevant
+2. **Abstract screening**: Read abstracts, apply inclusion/exclusion criteria
+3. **Full-text screening**: Obtain and review full texts
+4. Document reasons for exclusion at each stage
+
+### Phase 5: Quality Assessment
+1. Assess study quality using appropriate tools:
+ - **RCTs**: Cochrane Risk of Bias tool
+ - **Observational**: Newcastle-Ottawa Scale
+ - **Systematic reviews**: AMSTAR 2
+2. Grade quality of evidence (high, moderate, low, very low)
+3. Consider excluding very low-quality studies
+
+---
+
+## Search Documentation Template
+
+### Required Documentation
+All searches must be documented for reproducibility:
+
+```markdown
+## Search Strategy
+
+### Database: PubMed
+- **Date searched**: 2024-10-25
+- **Date range**: 2015-01-01 to 2024-10-25
+- **Search string**:
+ ```
+ ("CRISPR"[Title] OR "Cas9"[Title] OR "gene editing"[Title/Abstract])
+ AND ("sickle cell disease"[MeSH] OR "SCD"[Title/Abstract])
+ AND ("gene therapy"[MeSH] OR "therapeutic editing"[Title/Abstract])
+ AND 2015:2024[Publication Date]
+ AND English[Language]
+ ```
+- **Results**: 247 articles
+- **After deduplication**: 189 articles
+
+### Database: bioRxiv
+- **Date searched**: 2024-10-25
+- **Date range**: 2015-01-01 to 2024-10-25
+- **Search string**: "CRISPR" AND "sickle cell" (in title/abstract)
+- **Results**: 34 preprints
+- **After deduplication**: 28 preprints
+
+### Total Unique Articles
+- **Combined results**: 217 unique articles
+- **After title screening**: 156 articles
+- **After abstract screening**: 89 articles
+- **After full-text screening**: 52 articles included in review
+```
+
+---
+
+## Advanced Search Techniques
+
+### Citation Chaining
+
+#### Forward Citation Search
+Find papers that cite a key paper:
+- Use Google Scholar "Cited by" feature
+- Use OpenAlex or Semantic Scholar APIs
+- Identifies newer research building on seminal work
+
+#### Backward Citation Search
+Review references in key papers:
+- Extract references from included papers
+- Search for highly cited references
+- Identifies foundational research
+
+### Snowball Sampling
+1. Start with 3-5 highly relevant papers
+2. Extract all their references
+3. Check which references are cited by multiple papers
+4. Review those high-overlap references
+5. Repeat for newly identified key papers
+
+### Author Search
+Follow prolific authors in the field:
+- Search by author name across databases
+- Check author profiles (ORCID, Google Scholar)
+- Review recent publications and preprints
+
+### Related Article Features
+Many databases suggest related articles:
+- PubMed "Similar articles"
+- Semantic Scholar "Recommended papers"
+- Use to discover papers missed by keyword search
+
+---
+
+## Quality Control Checklist
+
+### Before Searching
+- [ ] Research question clearly defined
+- [ ] PICO criteria established (if applicable)
+- [ ] Search terms and synonyms listed
+- [ ] Inclusion/exclusion criteria documented
+- [ ] Target databases selected (minimum 3)
+- [ ] Date range determined
+
+### During Searching
+- [ ] Search string tested and refined
+- [ ] Results exported with complete metadata
+- [ ] Search parameters documented
+- [ ] Number of results recorded per database
+- [ ] Search date recorded
+
+### After Searching
+- [ ] Duplicates removed
+- [ ] Screening protocol followed
+- [ ] Reasons for exclusion documented
+- [ ] Quality assessment completed
+- [ ] All citations verified with verify_citations.py
+- [ ] Search methodology documented in review
+
+---
+
+## Common Pitfalls to Avoid
+
+1. **Too narrow search**: Missing relevant papers
+ - Solution: Include synonyms, related terms, broader concepts
+
+2. **Too broad search**: Thousands of irrelevant results
+ - Solution: Add specific concepts with AND, use field tags
+
+3. **Single database**: Incomplete coverage
+ - Solution: Search minimum 3 complementary databases
+
+4. **Ignoring preprints**: Missing latest findings
+ - Solution: Include bioRxiv, medRxiv, or arXiv
+
+5. **No documentation**: Irreproducible search
+ - Solution: Document every search string, date, and result count
+
+6. **Manual deduplication**: Time-consuming and error-prone
+ - Solution: Use search_databases.py script
+
+7. **Unverified citations**: Broken DOIs, incorrect metadata
+ - Solution: Run verify_citations.py on final reference list
+
+8. **Publication bias**: Only including published positive results
+ - Solution: Search trial registries, contact authors for unpublished data
+
+---
+
+## Example Multi-Database Search Workflow
+
+```python
+# Example workflow using available skills
+
+# 1. Search PubMed via gget
+search_term = "CRISPR AND sickle cell disease"
+# Use gget search pubmed search_term
+
+# 2. Search bioRxiv
+# Use gget search biorxiv search_term
+
+# 3. Search arXiv for computational papers
+# Search arXiv with: cat:q-bio AND "CRISPR" AND "sickle cell"
+
+# 4. Search Semantic Scholar via API
+# Use semantic scholar API with search query
+
+# 5. Aggregate and deduplicate results
+# python search_databases.py combined_results.json --deduplicate --format markdown --output review_papers.md
+
+# 6. Verify all citations
+# python verify_citations.py review_papers.md
+
+# 7. Generate final PDF
+# python generate_pdf.py review_papers.md --citation-style nature
+```
+
+---
+
+## Resources
+
+### MeSH Browser
+https://meshb.nlm.nih.gov/search
+
+### Boolean Search Tutorial
+https://www.ncbi.nlm.nih.gov/books/NBK3827/
+
+### Citation Style Guides
+See references/citation_styles.md in this skill
+
+### PRISMA Guidelines
+Preferred Reporting Items for Systematic Reviews and Meta-Analyses:
+http://www.prisma-statement.org/
diff --git a/scientific-skills/literature-review/scripts/generate_pdf.py b/scientific-skills/literature-review/scripts/generate_pdf.py
new file mode 100644
index 0000000..b9cc7dd
--- /dev/null
+++ b/scientific-skills/literature-review/scripts/generate_pdf.py
@@ -0,0 +1,176 @@
+#!/usr/bin/env python3
+"""
+PDF Generation Script for Literature Reviews
+Converts markdown files to professionally formatted PDFs with proper styling.
+"""
+
+import subprocess
+import sys
+import os
+from pathlib import Path
+
+def generate_pdf(
+ markdown_file: str,
+ output_pdf: str = None,
+ citation_style: str = "apa",
+ template: str = None,
+ toc: bool = True,
+ number_sections: bool = True
+) -> bool:
+ """
+ Generate a PDF from a markdown file using pandoc.
+
+ Args:
+ markdown_file: Path to the markdown file
+ output_pdf: Path for output PDF (defaults to same name as markdown)
+ citation_style: Citation style (apa, nature, chicago, etc.)
+ template: Path to custom LaTeX template
+ toc: Include table of contents
+ number_sections: Number the sections
+
+ Returns:
+ True if successful, False otherwise
+ """
+
+ # Verify markdown file exists
+ if not os.path.exists(markdown_file):
+ print(f"Error: Markdown file not found: {markdown_file}")
+ return False
+
+ # Set default output path
+ if output_pdf is None:
+ output_pdf = Path(markdown_file).with_suffix('.pdf')
+
+ # Check if pandoc is installed
+ try:
+ subprocess.run(['pandoc', '--version'], capture_output=True, check=True)
+ except (subprocess.CalledProcessError, FileNotFoundError):
+ print("Error: pandoc is not installed.")
+ print("Install with: brew install pandoc (macOS) or apt-get install pandoc (Linux)")
+ return False
+
+ # Build pandoc command
+ cmd = [
+ 'pandoc',
+ markdown_file,
+ '-o', str(output_pdf),
+ '--pdf-engine=xelatex', # Better Unicode support
+ '-V', 'geometry:margin=1in',
+ '-V', 'fontsize=11pt',
+ '-V', 'colorlinks=true',
+ '-V', 'linkcolor=blue',
+ '-V', 'urlcolor=blue',
+ '-V', 'citecolor=blue',
+ ]
+
+ # Add table of contents
+ if toc:
+ cmd.extend(['--toc', '--toc-depth=3'])
+
+ # Add section numbering
+ if number_sections:
+ cmd.append('--number-sections')
+
+ # Add citation processing if bibliography exists
+ bib_file = Path(markdown_file).with_suffix('.bib')
+ if bib_file.exists():
+ cmd.extend([
+ '--citeproc',
+ '--bibliography', str(bib_file),
+ '--csl', f'{citation_style}.csl' if not citation_style.endswith('.csl') else citation_style
+ ])
+
+ # Add custom template if provided
+ if template and os.path.exists(template):
+ cmd.extend(['--template', template])
+
+ # Execute pandoc
+ try:
+ print(f"Generating PDF: {output_pdf}")
+ print(f"Command: {' '.join(cmd)}")
+ result = subprocess.run(cmd, capture_output=True, text=True, check=True)
+ print(f"✓ PDF generated successfully: {output_pdf}")
+ return True
+ except subprocess.CalledProcessError as e:
+ print(f"Error generating PDF:")
+ print(f"STDOUT: {e.stdout}")
+ print(f"STDERR: {e.stderr}")
+ return False
+
+def check_dependencies():
+ """Check if required dependencies are installed."""
+ dependencies = {
+ 'pandoc': 'pandoc --version',
+ 'xelatex': 'xelatex --version'
+ }
+
+ missing = []
+ for name, cmd in dependencies.items():
+ try:
+ subprocess.run(cmd.split(), capture_output=True, check=True)
+ print(f"✓ {name} is installed")
+ except (subprocess.CalledProcessError, FileNotFoundError):
+ print(f"✗ {name} is NOT installed")
+ missing.append(name)
+
+ if missing:
+ print("\n" + "="*60)
+ print("Missing dependencies:")
+ for dep in missing:
+ if dep == 'pandoc':
+ print(" - pandoc: brew install pandoc (macOS) or apt-get install pandoc (Linux)")
+ elif dep == 'xelatex':
+ print(" - xelatex: brew install --cask mactex (macOS) or apt-get install texlive-xetex (Linux)")
+ return False
+
+ return True
+
+def main():
+ """Command-line interface."""
+ if len(sys.argv) < 2:
+ print("Usage: python generate_pdf.py [output_pdf] [--citation-style STYLE]")
+ print("\nOptions:")
+ print(" --citation-style STYLE Citation style (default: apa)")
+ print(" --no-toc Disable table of contents")
+ print(" --no-numbers Disable section numbering")
+ print(" --check-deps Check if dependencies are installed")
+ sys.exit(1)
+
+ # Check dependencies mode
+ if '--check-deps' in sys.argv:
+ check_dependencies()
+ sys.exit(0)
+
+ # Parse arguments
+ markdown_file = sys.argv[1]
+ output_pdf = sys.argv[2] if len(sys.argv) > 2 and not sys.argv[2].startswith('--') else None
+
+ citation_style = 'apa'
+ toc = True
+ number_sections = True
+
+ # Parse optional flags
+ if '--citation-style' in sys.argv:
+ idx = sys.argv.index('--citation-style')
+ if idx + 1 < len(sys.argv):
+ citation_style = sys.argv[idx + 1]
+
+ if '--no-toc' in sys.argv:
+ toc = False
+
+ if '--no-numbers' in sys.argv:
+ number_sections = False
+
+ # Generate PDF
+ success = generate_pdf(
+ markdown_file,
+ output_pdf,
+ citation_style=citation_style,
+ toc=toc,
+ number_sections=number_sections
+ )
+
+ sys.exit(0 if success else 1)
+
+if __name__ == "__main__":
+ main()
diff --git a/scientific-skills/literature-review/scripts/search_databases.py b/scientific-skills/literature-review/scripts/search_databases.py
new file mode 100644
index 0000000..19081cd
--- /dev/null
+++ b/scientific-skills/literature-review/scripts/search_databases.py
@@ -0,0 +1,303 @@
+#!/usr/bin/env python3
+"""
+Literature Database Search Script
+Searches multiple literature databases and aggregates results.
+"""
+
+import json
+import sys
+from typing import Dict, List
+from datetime import datetime
+
+def format_search_results(results: List[Dict], output_format: str = 'json') -> str:
+ """
+ Format search results for output.
+
+ Args:
+ results: List of search results
+ output_format: Format (json, markdown, or bibtex)
+
+ Returns:
+ Formatted string
+ """
+ if output_format == 'json':
+ return json.dumps(results, indent=2)
+
+ elif output_format == 'markdown':
+ md = f"# Literature Search Results\n\n"
+ md += f"**Search Date**: {datetime.now().strftime('%Y-%m-%d %H:%M')}\n"
+ md += f"**Total Results**: {len(results)}\n\n"
+
+ for i, result in enumerate(results, 1):
+ md += f"## {i}. {result.get('title', 'Untitled')}\n\n"
+ md += f"**Authors**: {result.get('authors', 'Unknown')}\n\n"
+ md += f"**Year**: {result.get('year', 'N/A')}\n\n"
+ md += f"**Source**: {result.get('source', 'Unknown')}\n\n"
+
+ if result.get('abstract'):
+ md += f"**Abstract**: {result['abstract']}\n\n"
+
+ if result.get('doi'):
+ md += f"**DOI**: [{result['doi']}](https://doi.org/{result['doi']})\n\n"
+
+ if result.get('url'):
+ md += f"**URL**: {result['url']}\n\n"
+
+ if result.get('citations'):
+ md += f"**Citations**: {result['citations']}\n\n"
+
+ md += "---\n\n"
+
+ return md
+
+ elif output_format == 'bibtex':
+ bibtex = ""
+ for i, result in enumerate(results, 1):
+ entry_type = result.get('type', 'article')
+ cite_key = f"{result.get('first_author', 'unknown')}{result.get('year', '0000')}"
+
+ bibtex += f"@{entry_type}{{{cite_key},\n"
+ bibtex += f" title = {{{result.get('title', '')}}},\n"
+ bibtex += f" author = {{{result.get('authors', '')}}},\n"
+ bibtex += f" year = {{{result.get('year', '')}}},\n"
+
+ if result.get('journal'):
+ bibtex += f" journal = {{{result['journal']}}},\n"
+
+ if result.get('volume'):
+ bibtex += f" volume = {{{result['volume']}}},\n"
+
+ if result.get('pages'):
+ bibtex += f" pages = {{{result['pages']}}},\n"
+
+ if result.get('doi'):
+ bibtex += f" doi = {{{result['doi']}}},\n"
+
+ bibtex += "}\n\n"
+
+ return bibtex
+
+ else:
+ raise ValueError(f"Unknown format: {output_format}")
+
+def deduplicate_results(results: List[Dict]) -> List[Dict]:
+ """
+ Remove duplicate results based on DOI or title.
+
+ Args:
+ results: List of search results
+
+ Returns:
+ Deduplicated list
+ """
+ seen_dois = set()
+ seen_titles = set()
+ unique_results = []
+
+ for result in results:
+ doi = result.get('doi', '').lower().strip()
+ title = result.get('title', '').lower().strip()
+
+ # Check DOI first (more reliable)
+ if doi and doi in seen_dois:
+ continue
+
+ # Check title as fallback
+ if not doi and title in seen_titles:
+ continue
+
+ # Add to results
+ if doi:
+ seen_dois.add(doi)
+ if title:
+ seen_titles.add(title)
+
+ unique_results.append(result)
+
+ return unique_results
+
+def rank_results(results: List[Dict], criteria: str = 'citations') -> List[Dict]:
+ """
+ Rank results by specified criteria.
+
+ Args:
+ results: List of search results
+ criteria: Ranking criteria (citations, year, relevance)
+
+ Returns:
+ Ranked list
+ """
+ if criteria == 'citations':
+ return sorted(results, key=lambda x: x.get('citations', 0), reverse=True)
+ elif criteria == 'year':
+ return sorted(results, key=lambda x: x.get('year', '0'), reverse=True)
+ elif criteria == 'relevance':
+ return sorted(results, key=lambda x: x.get('relevance_score', 0), reverse=True)
+ else:
+ return results
+
+def filter_by_year(results: List[Dict], start_year: int = None, end_year: int = None) -> List[Dict]:
+ """
+ Filter results by publication year range.
+
+ Args:
+ results: List of search results
+ start_year: Minimum year (inclusive)
+ end_year: Maximum year (inclusive)
+
+ Returns:
+ Filtered list
+ """
+ filtered = []
+
+ for result in results:
+ try:
+ year = int(result.get('year', 0))
+ if start_year and year < start_year:
+ continue
+ if end_year and year > end_year:
+ continue
+ filtered.append(result)
+ except (ValueError, TypeError):
+ # Include if year parsing fails
+ filtered.append(result)
+
+ return filtered
+
+def generate_search_summary(results: List[Dict]) -> Dict:
+ """
+ Generate summary statistics for search results.
+
+ Args:
+ results: List of search results
+
+ Returns:
+ Summary dictionary
+ """
+ summary = {
+ 'total_results': len(results),
+ 'sources': {},
+ 'year_distribution': {},
+ 'avg_citations': 0,
+ 'total_citations': 0
+ }
+
+ citations = []
+
+ for result in results:
+ # Count by source
+ source = result.get('source', 'Unknown')
+ summary['sources'][source] = summary['sources'].get(source, 0) + 1
+
+ # Count by year
+ year = result.get('year', 'Unknown')
+ summary['year_distribution'][year] = summary['year_distribution'].get(year, 0) + 1
+
+ # Collect citations
+ if result.get('citations'):
+ try:
+ citations.append(int(result['citations']))
+ except (ValueError, TypeError):
+ pass
+
+ if citations:
+ summary['avg_citations'] = sum(citations) / len(citations)
+ summary['total_citations'] = sum(citations)
+
+ return summary
+
+def main():
+ """Command-line interface for search result processing."""
+ if len(sys.argv) < 2:
+ print("Usage: python search_databases.py [options]")
+ print("\nOptions:")
+ print(" --format FORMAT Output format (json, markdown, bibtex)")
+ print(" --output FILE Output file (default: stdout)")
+ print(" --rank CRITERIA Rank by (citations, year, relevance)")
+ print(" --year-start YEAR Filter by start year")
+ print(" --year-end YEAR Filter by end year")
+ print(" --deduplicate Remove duplicates")
+ print(" --summary Show summary statistics")
+ sys.exit(1)
+
+ # Load results
+ results_file = sys.argv[1]
+ try:
+ with open(results_file, 'r', encoding='utf-8') as f:
+ results = json.load(f)
+ except Exception as e:
+ print(f"Error loading results: {e}")
+ sys.exit(1)
+
+ # Parse options
+ output_format = 'markdown'
+ output_file = None
+ rank_criteria = None
+ year_start = None
+ year_end = None
+ do_dedup = False
+ show_summary = False
+
+ i = 2
+ while i < len(sys.argv):
+ arg = sys.argv[i]
+
+ if arg == '--format' and i + 1 < len(sys.argv):
+ output_format = sys.argv[i + 1]
+ i += 2
+ elif arg == '--output' and i + 1 < len(sys.argv):
+ output_file = sys.argv[i + 1]
+ i += 2
+ elif arg == '--rank' and i + 1 < len(sys.argv):
+ rank_criteria = sys.argv[i + 1]
+ i += 2
+ elif arg == '--year-start' and i + 1 < len(sys.argv):
+ year_start = int(sys.argv[i + 1])
+ i += 2
+ elif arg == '--year-end' and i + 1 < len(sys.argv):
+ year_end = int(sys.argv[i + 1])
+ i += 2
+ elif arg == '--deduplicate':
+ do_dedup = True
+ i += 1
+ elif arg == '--summary':
+ show_summary = True
+ i += 1
+ else:
+ i += 1
+
+ # Process results
+ if do_dedup:
+ results = deduplicate_results(results)
+ print(f"After deduplication: {len(results)} results")
+
+ if year_start or year_end:
+ results = filter_by_year(results, year_start, year_end)
+ print(f"After year filter: {len(results)} results")
+
+ if rank_criteria:
+ results = rank_results(results, rank_criteria)
+ print(f"Ranked by: {rank_criteria}")
+
+ # Show summary
+ if show_summary:
+ summary = generate_search_summary(results)
+ print("\n" + "="*60)
+ print("SEARCH SUMMARY")
+ print("="*60)
+ print(json.dumps(summary, indent=2))
+ print()
+
+ # Format output
+ output = format_search_results(results, output_format)
+
+ # Write output
+ if output_file:
+ with open(output_file, 'w', encoding='utf-8') as f:
+ f.write(output)
+ print(f"✓ Results saved to: {output_file}")
+ else:
+ print(output)
+
+if __name__ == "__main__":
+ main()
diff --git a/scientific-skills/literature-review/scripts/verify_citations.py b/scientific-skills/literature-review/scripts/verify_citations.py
new file mode 100644
index 0000000..ee6e4d5
--- /dev/null
+++ b/scientific-skills/literature-review/scripts/verify_citations.py
@@ -0,0 +1,222 @@
+#!/usr/bin/env python3
+"""
+Citation Verification Script
+Verifies DOIs, URLs, and citation metadata for accuracy.
+"""
+
+import re
+import requests
+import json
+from typing import Dict, List, Tuple
+from urllib.parse import urlparse
+import time
+
+class CitationVerifier:
+ def __init__(self):
+ self.session = requests.Session()
+ self.session.headers.update({
+ 'User-Agent': 'CitationVerifier/1.0 (Literature Review Tool)'
+ })
+
+ def extract_dois(self, text: str) -> List[str]:
+ """Extract all DOIs from text."""
+ doi_pattern = r'10\.\d{4,}/[^\s\]\)"]+'
+ return re.findall(doi_pattern, text)
+
+ def verify_doi(self, doi: str) -> Tuple[bool, Dict]:
+ """
+ Verify a DOI and retrieve metadata.
+ Returns (is_valid, metadata)
+ """
+ try:
+ url = f"https://doi.org/api/handles/{doi}"
+ response = self.session.get(url, timeout=10)
+
+ if response.status_code == 200:
+ # DOI exists, now get metadata from CrossRef
+ metadata = self._get_crossref_metadata(doi)
+ return True, metadata
+ else:
+ return False, {}
+ except Exception as e:
+ return False, {"error": str(e)}
+
+ def _get_crossref_metadata(self, doi: str) -> Dict:
+ """Get metadata from CrossRef API."""
+ try:
+ url = f"https://api.crossref.org/works/{doi}"
+ response = self.session.get(url, timeout=10)
+
+ if response.status_code == 200:
+ data = response.json()
+ message = data.get('message', {})
+
+ # Extract key metadata
+ metadata = {
+ 'title': message.get('title', [''])[0],
+ 'authors': self._format_authors(message.get('author', [])),
+ 'year': self._extract_year(message),
+ 'journal': message.get('container-title', [''])[0],
+ 'volume': message.get('volume', ''),
+ 'pages': message.get('page', ''),
+ 'doi': doi
+ }
+ return metadata
+ return {}
+ except Exception as e:
+ return {"error": str(e)}
+
+ def _format_authors(self, authors: List[Dict]) -> str:
+ """Format author list."""
+ if not authors:
+ return ""
+
+ formatted = []
+ for author in authors[:3]: # First 3 authors
+ given = author.get('given', '')
+ family = author.get('family', '')
+ if family:
+ formatted.append(f"{family}, {given[0]}." if given else family)
+
+ if len(authors) > 3:
+ formatted.append("et al.")
+
+ return ", ".join(formatted)
+
+ def _extract_year(self, message: Dict) -> str:
+ """Extract publication year."""
+ date_parts = message.get('published-print', {}).get('date-parts', [[]])
+ if not date_parts or not date_parts[0]:
+ date_parts = message.get('published-online', {}).get('date-parts', [[]])
+
+ if date_parts and date_parts[0]:
+ return str(date_parts[0][0])
+ return ""
+
+ def verify_url(self, url: str) -> Tuple[bool, int]:
+ """
+ Verify a URL is accessible.
+ Returns (is_accessible, status_code)
+ """
+ try:
+ response = self.session.head(url, timeout=10, allow_redirects=True)
+ is_accessible = response.status_code < 400
+ return is_accessible, response.status_code
+ except Exception as e:
+ return False, 0
+
+ def verify_citations_in_file(self, filepath: str) -> Dict:
+ """
+ Verify all citations in a markdown file.
+ Returns a report of verification results.
+ """
+ with open(filepath, 'r', encoding='utf-8') as f:
+ content = f.read()
+
+ dois = self.extract_dois(content)
+
+ report = {
+ 'total_dois': len(dois),
+ 'verified': [],
+ 'failed': [],
+ 'metadata': {}
+ }
+
+ for doi in dois:
+ print(f"Verifying DOI: {doi}")
+ is_valid, metadata = self.verify_doi(doi)
+
+ if is_valid:
+ report['verified'].append(doi)
+ report['metadata'][doi] = metadata
+ else:
+ report['failed'].append(doi)
+
+ time.sleep(0.5) # Rate limiting
+
+ return report
+
+ def format_citation_apa(self, metadata: Dict) -> str:
+ """Format citation in APA style."""
+ authors = metadata.get('authors', '')
+ year = metadata.get('year', 'n.d.')
+ title = metadata.get('title', '')
+ journal = metadata.get('journal', '')
+ volume = metadata.get('volume', '')
+ pages = metadata.get('pages', '')
+ doi = metadata.get('doi', '')
+
+ citation = f"{authors} ({year}). {title}. "
+ if journal:
+ citation += f"*{journal}*"
+ if volume:
+ citation += f", *{volume}*"
+ if pages:
+ citation += f", {pages}"
+ if doi:
+ citation += f". https://doi.org/{doi}"
+
+ return citation
+
+ def format_citation_nature(self, metadata: Dict) -> str:
+ """Format citation in Nature style."""
+ authors = metadata.get('authors', '')
+ title = metadata.get('title', '')
+ journal = metadata.get('journal', '')
+ volume = metadata.get('volume', '')
+ pages = metadata.get('pages', '')
+ year = metadata.get('year', '')
+
+ citation = f"{authors} {title}. "
+ if journal:
+ citation += f"*{journal}* "
+ if volume:
+ citation += f"**{volume}**, "
+ if pages:
+ citation += f"{pages} "
+ if year:
+ citation += f"({year})"
+
+ return citation
+
+def main():
+ """Example usage."""
+ import sys
+
+ if len(sys.argv) < 2:
+ print("Usage: python verify_citations.py ")
+ sys.exit(1)
+
+ filepath = sys.argv[1]
+ verifier = CitationVerifier()
+
+ print(f"Verifying citations in: {filepath}")
+ report = verifier.verify_citations_in_file(filepath)
+
+ print("\n" + "="*60)
+ print("CITATION VERIFICATION REPORT")
+ print("="*60)
+ print(f"\nTotal DOIs found: {report['total_dois']}")
+ print(f"Verified: {len(report['verified'])}")
+ print(f"Failed: {len(report['failed'])}")
+
+ if report['failed']:
+ print("\nFailed DOIs:")
+ for doi in report['failed']:
+ print(f" - {doi}")
+
+ if report['metadata']:
+ print("\n\nVerified Citations (APA format):")
+ for doi, metadata in report['metadata'].items():
+ citation = verifier.format_citation_apa(metadata)
+ print(f"\n{citation}")
+
+ # Save detailed report
+ output_file = filepath.replace('.md', '_citation_report.json')
+ with open(output_file, 'w', encoding='utf-8') as f:
+ json.dump(report, f, indent=2)
+
+ print(f"\n\nDetailed report saved to: {output_file}")
+
+if __name__ == "__main__":
+ main()
diff --git a/scientific-skills/market-research-reports/SKILL.md b/scientific-skills/market-research-reports/SKILL.md
new file mode 100644
index 0000000..90435c0
--- /dev/null
+++ b/scientific-skills/market-research-reports/SKILL.md
@@ -0,0 +1,901 @@
+---
+name: market-research-reports
+description: "Generate comprehensive market research reports (50+ pages) in the style of top consulting firms (McKinsey, BCG, Gartner). Features professional LaTeX formatting, extensive visual generation with scientific-schematics and generate-image, deep integration with research-lookup for data gathering, and multi-framework strategic analysis including Porter's Five Forces, PESTLE, SWOT, TAM/SAM/SOM, and BCG Matrix."
+allowed-tools: [Read, Write, Edit, Bash]
+---
+
+# Market Research Reports
+
+## Overview
+
+Market research reports are comprehensive strategic documents that analyze industries, markets, and competitive landscapes to inform business decisions, investment strategies, and strategic planning. This skill generates **professional-grade reports of 50+ pages** with extensive visual content, modeled after deliverables from top consulting firms like McKinsey, BCG, Bain, Gartner, and Forrester.
+
+**Key Features:**
+- **Comprehensive length**: Reports are designed to be 50+ pages with no token constraints
+- **Visual-rich content**: 5-6 key diagrams generated at start (more added as needed during writing)
+- **Data-driven analysis**: Deep integration with research-lookup for market data
+- **Multi-framework approach**: Porter's Five Forces, PESTLE, SWOT, BCG Matrix, TAM/SAM/SOM
+- **Professional formatting**: Consulting-firm quality typography, colors, and layout
+- **Actionable recommendations**: Strategic focus with implementation roadmaps
+
+**Output Format:** LaTeX with professional styling, compiled to PDF. Uses the `market_research.sty` style package for consistent, professional formatting.
+
+## When to Use This Skill
+
+This skill should be used when:
+- Creating comprehensive market analysis for investment decisions
+- Developing industry reports for strategic planning
+- Analyzing competitive landscapes and market dynamics
+- Conducting market sizing exercises (TAM/SAM/SOM)
+- Evaluating market entry opportunities
+- Preparing due diligence materials for M&A activities
+- Creating thought leadership content for industry positioning
+- Developing go-to-market strategy documentation
+- Analyzing regulatory and policy impacts on markets
+- Building business cases for new product launches
+
+## Visual Enhancement Requirements
+
+**CRITICAL: Market research reports should include key visual content.**
+
+Every report should generate **6 essential visuals** at the start, with additional visuals added as needed during writing. Start with the most critical visualizations to establish the report framework.
+
+### Visual Generation Tools
+
+**Use `scientific-schematics` for:**
+- Market growth trajectory charts
+- TAM/SAM/SOM breakdown diagrams (concentric circles)
+- Porter's Five Forces diagrams
+- Competitive positioning matrices
+- Market segmentation charts
+- Value chain diagrams
+- Technology roadmaps
+- Risk heatmaps
+- Strategic prioritization matrices
+- Implementation timelines/Gantt charts
+- SWOT analysis diagrams
+- BCG Growth-Share matrices
+
+```bash
+# Example: Generate a TAM/SAM/SOM diagram
+python skills/scientific-schematics/scripts/generate_schematic.py \
+ "TAM SAM SOM concentric circle diagram showing Total Addressable Market $50B outer circle, Serviceable Addressable Market $15B middle circle, Serviceable Obtainable Market $3B inner circle, with labels and arrows pointing to each segment" \
+ -o figures/tam_sam_som.png --doc-type report
+
+# Example: Generate Porter's Five Forces
+python skills/scientific-schematics/scripts/generate_schematic.py \
+ "Porter's Five Forces diagram with center box 'Competitive Rivalry' connected to four surrounding boxes: 'Threat of New Entrants' (top), 'Bargaining Power of Suppliers' (left), 'Bargaining Power of Buyers' (right), 'Threat of Substitutes' (bottom). Each box should show High/Medium/Low rating" \
+ -o figures/porters_five_forces.png --doc-type report
+```
+
+**Use `generate-image` for:**
+- Executive summary hero infographics
+- Industry/sector conceptual illustrations
+- Abstract technology visualizations
+- Cover page imagery
+
+```bash
+# Example: Generate executive summary infographic
+python skills/generate-image/scripts/generate_image.py \
+ "Professional executive summary infographic for market research report, showing key metrics in modern data visualization style, blue and green color scheme, clean minimalist design with icons representing market size, growth rate, and competitive landscape" \
+ --output figures/executive_summary.png
+```
+
+### Recommended Visuals by Section (Generate as Needed)
+
+| Section | Priority Visuals | Optional Visuals |
+|---------|-----------------|------------------|
+| Executive Summary | Executive infographic (START) | - |
+| Market Size & Growth | Growth trajectory (START), TAM/SAM/SOM (START) | Regional breakdown, segment growth |
+| Competitive Landscape | Porter's Five Forces (START), Positioning matrix (START) | Market share chart, strategic groups |
+| Risk Analysis | Risk heatmap (START) | Mitigation matrix |
+| Strategic Recommendations | Opportunity matrix | Priority framework |
+| Implementation Roadmap | Timeline/Gantt | Milestone tracker |
+| Investment Thesis | Financial projections | Scenario analysis |
+
+**Start with 6 priority visuals** (marked as START above), then generate additional visuals as specific sections are written and require visual support.
+
+---
+
+## Report Structure (50+ Pages)
+
+### Front Matter (~5 pages)
+
+#### Cover Page (1 page)
+- Report title and subtitle
+- Hero visualization (generated)
+- Date and classification
+- Prepared for / Prepared by
+
+#### Table of Contents (1-2 pages)
+- Automated from LaTeX
+- List of Figures
+- List of Tables
+
+#### Executive Summary (2-3 pages)
+- **Market Snapshot Box**: Key metrics at a glance
+- **Investment Thesis**: 3-5 bullet point summary
+- **Key Findings**: Major discoveries and insights
+- **Strategic Recommendations**: Top 3-5 actionable recommendations
+- **Executive Summary Infographic**: Visual synthesis of report highlights
+
+---
+
+### Core Analysis (~35 pages)
+
+#### Chapter 1: Market Overview & Definition (4-5 pages)
+
+**Content Requirements:**
+- Market definition and scope
+- Industry ecosystem mapping
+- Key stakeholders and their roles
+- Market boundaries and adjacencies
+- Historical context and evolution
+
+**Required Visuals (2):**
+1. Market ecosystem/value chain diagram
+2. Industry structure diagram
+
+**Key Data Points:**
+- Market definition criteria
+- Included/excluded segments
+- Geographic scope
+- Time horizon for analysis
+
+---
+
+#### Chapter 2: Market Size & Growth Analysis (6-8 pages)
+
+**Content Requirements:**
+- Total Addressable Market (TAM) calculation
+- Serviceable Addressable Market (SAM) definition
+- Serviceable Obtainable Market (SOM) estimation
+- Historical growth analysis (5-10 years)
+- Growth projections (5-10 years forward)
+- Growth drivers and inhibitors
+- Regional market breakdown
+- Segment-level analysis
+
+**Required Visuals (4):**
+1. Market growth trajectory chart (historical + projected)
+2. TAM/SAM/SOM concentric circles diagram
+3. Regional market breakdown (pie chart or treemap)
+4. Segment growth comparison (bar chart)
+
+**Key Data Points:**
+- Current market size (with source)
+- CAGR (historical and projected)
+- Market size by region
+- Market size by segment
+- Key assumptions for projections
+
+**Data Sources:**
+Use `research-lookup` to find:
+- Market research reports (Gartner, Forrester, IDC, etc.)
+- Industry association data
+- Government statistics
+- Company financial reports
+- Academic studies
+
+---
+
+#### Chapter 3: Industry Drivers & Trends (5-6 pages)
+
+**Content Requirements:**
+- Macroeconomic factors
+- Technology trends
+- Regulatory drivers
+- Social and demographic shifts
+- Environmental factors
+- Industry-specific trends
+
+**Analysis Frameworks:**
+- **PESTLE Analysis**: Political, Economic, Social, Technological, Legal, Environmental
+- **Trend Impact Assessment**: Likelihood vs Impact matrix
+
+**Required Visuals (3):**
+1. Industry trends timeline or radar chart
+2. Driver impact matrix
+3. PESTLE analysis diagram
+
+**Key Data Points:**
+- Top 5-10 growth drivers with quantified impact
+- Emerging trends with timeline
+- Disruption factors
+
+---
+
+#### Chapter 4: Competitive Landscape (6-8 pages)
+
+**Content Requirements:**
+- Market structure analysis
+- Major player profiles
+- Market share analysis
+- Competitive positioning
+- Barriers to entry
+- Competitive dynamics
+
+**Analysis Frameworks:**
+- **Porter's Five Forces**: Comprehensive industry analysis
+- **Competitive Positioning Matrix**: 2x2 matrix on key dimensions
+- **Strategic Group Mapping**: Cluster competitors by strategy
+
+**Required Visuals (4):**
+1. Porter's Five Forces diagram
+2. Market share pie chart or bar chart
+3. Competitive positioning matrix (2x2)
+4. Strategic group map
+
+**Key Data Points:**
+- Market share by company (top 10)
+- Competitive intensity rating
+- Entry barriers assessment
+- Supplier/buyer power assessment
+
+---
+
+#### Chapter 5: Customer Analysis & Segmentation (4-5 pages)
+
+**Content Requirements:**
+- Customer segment definitions
+- Segment size and growth
+- Buying behavior analysis
+- Customer needs and pain points
+- Decision-making process
+- Value drivers by segment
+
+**Analysis Frameworks:**
+- **Customer Segmentation Matrix**: Size vs Growth
+- **Value Proposition Canvas**: Jobs, Pains, Gains
+- **Customer Journey Mapping**: Awareness to Advocacy
+
+**Required Visuals (3):**
+1. Customer segmentation breakdown (pie/treemap)
+2. Segment attractiveness matrix
+3. Customer journey or value proposition diagram
+
+**Key Data Points:**
+- Segment sizes and percentages
+- Growth rates by segment
+- Average deal size / revenue per customer
+- Customer acquisition cost by segment
+
+---
+
+#### Chapter 6: Technology & Innovation Landscape (4-5 pages)
+
+**Content Requirements:**
+- Current technology stack
+- Emerging technologies
+- Innovation trends
+- Technology adoption curves
+- R&D investment analysis
+- Patent landscape
+
+**Analysis Frameworks:**
+- **Technology Readiness Assessment**: TRL levels
+- **Hype Cycle Positioning**: Where technologies sit
+- **Technology Roadmap**: Evolution over time
+
+**Required Visuals (2):**
+1. Technology roadmap diagram
+2. Innovation/adoption curve or hype cycle
+
+**Key Data Points:**
+- R&D spending in the industry
+- Key technology milestones
+- Patent filing trends
+- Technology adoption rates
+
+---
+
+#### Chapter 7: Regulatory & Policy Environment (3-4 pages)
+
+**Content Requirements:**
+- Current regulatory framework
+- Key regulatory bodies
+- Compliance requirements
+- Upcoming regulatory changes
+- Policy trends
+- Impact assessment
+
+**Required Visuals (1):**
+1. Regulatory timeline or framework diagram
+
+**Key Data Points:**
+- Key regulations and effective dates
+- Compliance costs
+- Regulatory risks
+- Policy change probability
+
+---
+
+#### Chapter 8: Risk Analysis (3-4 pages)
+
+**Content Requirements:**
+- Market risks
+- Competitive risks
+- Regulatory risks
+- Technology risks
+- Operational risks
+- Financial risks
+- Risk mitigation strategies
+
+**Analysis Frameworks:**
+- **Risk Heatmap**: Probability vs Impact
+- **Risk Register**: Comprehensive risk inventory
+- **Mitigation Matrix**: Risk vs Mitigation strategy
+
+**Required Visuals (2):**
+1. Risk heatmap (probability vs impact)
+2. Risk mitigation matrix
+
+**Key Data Points:**
+- Top 10 risks with ratings
+- Risk probability scores
+- Impact severity scores
+- Mitigation cost estimates
+
+---
+
+### Strategic Recommendations (~10 pages)
+
+#### Chapter 9: Strategic Opportunities & Recommendations (4-5 pages)
+
+**Content Requirements:**
+- Opportunity identification
+- Opportunity sizing
+- Strategic options analysis
+- Prioritization framework
+- Detailed recommendations
+- Success factors
+
+**Analysis Frameworks:**
+- **Opportunity Attractiveness Matrix**: Attractiveness vs Ability to Win
+- **Strategic Options Framework**: Build, Buy, Partner, Ignore
+- **Priority Matrix**: Impact vs Effort
+
+**Required Visuals (3):**
+1. Opportunity matrix
+2. Strategic options framework
+3. Priority/recommendation matrix
+
+**Key Data Points:**
+- Opportunity sizes
+- Investment requirements
+- Expected returns
+- Timeline to value
+
+---
+
+#### Chapter 10: Implementation Roadmap (3-4 pages)
+
+**Content Requirements:**
+- Phased implementation plan
+- Key milestones and deliverables
+- Resource requirements
+- Timeline and sequencing
+- Dependencies and critical path
+- Governance structure
+
+**Required Visuals (2):**
+1. Implementation timeline/Gantt chart
+2. Milestone tracker or phase diagram
+
+**Key Data Points:**
+- Phase durations
+- Resource requirements
+- Key milestones with dates
+- Budget allocation by phase
+
+---
+
+#### Chapter 11: Investment Thesis & Financial Projections (3-4 pages)
+
+**Content Requirements:**
+- Investment summary
+- Financial projections
+- Scenario analysis
+- Return expectations
+- Key assumptions
+- Sensitivity analysis
+
+**Required Visuals (2):**
+1. Financial projection chart (revenue, growth)
+2. Scenario analysis comparison
+
+**Key Data Points:**
+- Revenue projections (3-5 years)
+- CAGR projections
+- ROI/IRR expectations
+- Key financial assumptions
+
+---
+
+### Back Matter (~5 pages)
+
+#### Appendix A: Methodology & Data Sources (1-2 pages)
+- Research methodology
+- Data collection approach
+- Data sources and citations
+- Limitations and assumptions
+
+#### Appendix B: Detailed Market Data Tables (2-3 pages)
+- Comprehensive market data tables
+- Regional breakdowns
+- Segment details
+- Historical data series
+
+#### Appendix C: Company Profiles (1-2 pages)
+- Brief profiles of key competitors
+- Financial highlights
+- Strategic focus areas
+
+#### References/Bibliography
+- All sources cited
+- BibTeX format for LaTeX
+
+---
+
+## Workflow
+
+### Phase 1: Research & Data Gathering
+
+**Step 1: Define Scope**
+- Clarify market definition
+- Set geographic boundaries
+- Determine time horizon
+- Identify key questions to answer
+
+**Step 2: Conduct Deep Research**
+
+Use `research-lookup` extensively to gather market data:
+
+```bash
+# Market size and growth data
+python skills/research-lookup/scripts/research_lookup.py \
+ "What is the current market size and projected growth rate for [MARKET] industry? Include TAM, SAM, SOM estimates and CAGR projections"
+
+# Competitive landscape
+python skills/research-lookup/scripts/research_lookup.py \
+ "Who are the top 10 competitors in the [MARKET] market? What is their market share and competitive positioning?"
+
+# Industry trends
+python skills/research-lookup/scripts/research_lookup.py \
+ "What are the major trends and growth drivers in the [MARKET] industry for 2024-2030?"
+
+# Regulatory environment
+python skills/research-lookup/scripts/research_lookup.py \
+ "What are the key regulations and policy changes affecting the [MARKET] industry?"
+```
+
+**Step 3: Data Organization**
+- Create `sources/` folder with research notes
+- Organize data by section
+- Identify data gaps
+- Conduct follow-up research as needed
+
+### Phase 2: Analysis & Framework Application
+
+**Step 4: Apply Analysis Frameworks**
+
+For each framework, conduct structured analysis:
+
+- **Market Sizing**: TAM → SAM → SOM with clear assumptions
+- **Porter's Five Forces**: Rate each force High/Medium/Low with rationale
+- **PESTLE**: Analyze each dimension with trends and impacts
+- **SWOT**: Internal strengths/weaknesses, external opportunities/threats
+- **Competitive Positioning**: Define axes, plot competitors
+
+**Step 5: Develop Insights**
+- Synthesize findings into key insights
+- Identify strategic implications
+- Develop recommendations
+- Prioritize opportunities
+
+### Phase 3: Visual Generation
+
+**Step 6: Generate All Visuals**
+
+Generate visuals BEFORE writing the report. Use the batch generation script:
+
+```bash
+# Generate all standard market report visuals
+python skills/market-research-reports/scripts/generate_market_visuals.py \
+ --topic "[MARKET NAME]" \
+ --output-dir figures/
+```
+
+Or generate individually:
+
+```bash
+# 1. Market growth trajectory
+python skills/scientific-schematics/scripts/generate_schematic.py \
+ "Bar chart showing market growth from 2020 to 2034, with historical bars in dark blue (2020-2024) and projected bars in light blue (2025-2034). Y-axis shows market size in billions USD. Include CAGR annotation" \
+ -o figures/01_market_growth.png --doc-type report
+
+# 2. TAM/SAM/SOM breakdown
+python skills/scientific-schematics/scripts/generate_schematic.py \
+ "TAM SAM SOM concentric circles diagram. Outer circle TAM Total Addressable Market, middle circle SAM Serviceable Addressable Market, inner circle SOM Serviceable Obtainable Market. Each labeled with acronym and description. Blue gradient" \
+ -o figures/02_tam_sam_som.png --doc-type report
+
+# 3. Porter's Five Forces
+python skills/scientific-schematics/scripts/generate_schematic.py \
+ "Porter's Five Forces diagram with center box 'Competitive Rivalry' connected to four surrounding boxes: Threat of New Entrants (top), Bargaining Power of Suppliers (left), Bargaining Power of Buyers (right), Threat of Substitutes (bottom). Color code by rating: High=red, Medium=yellow, Low=green" \
+ -o figures/03_porters_five_forces.png --doc-type report
+
+# 4. Competitive positioning matrix
+python skills/scientific-schematics/scripts/generate_schematic.py \
+ "2x2 competitive positioning matrix with X-axis 'Market Focus (Niche to Broad)' and Y-axis 'Solution Approach (Product to Platform)'. Plot 8-10 competitors as labeled circles of varying sizes. Include quadrant labels" \
+ -o figures/04_competitive_positioning.png --doc-type report
+
+# 5. Risk heatmap
+python skills/scientific-schematics/scripts/generate_schematic.py \
+ "Risk heatmap matrix. X-axis Impact (Low to Critical), Y-axis Probability (Unlikely to Very Likely). Color gradient: Green (low risk) to Red (critical risk). Plot 10-12 risks as labeled points" \
+ -o figures/05_risk_heatmap.png --doc-type report
+
+# 6. (Optional) Executive summary infographic
+python skills/generate-image/scripts/generate_image.py \
+ "Professional executive summary infographic for market research report, modern data visualization style, blue and green color scheme, clean minimalist design" \
+ --output figures/06_exec_summary.png
+```
+
+### Phase 4: Report Writing
+
+**Step 7: Initialize Project Structure**
+
+Create the standard project structure:
+
+```
+writing_outputs/YYYYMMDD_HHMMSS_market_report_[topic]/
+├── progress.md
+├── drafts/
+│ └── v1_market_report.tex
+├── references/
+│ └── references.bib
+├── figures/
+│ └── [all generated visuals]
+├── sources/
+│ └── [research notes]
+└── final/
+```
+
+**Step 8: Write Report Using Template**
+
+Use the `market_report_template.tex` as a starting point. Write each section following the structure guide, ensuring:
+
+- **Comprehensive coverage**: Every subsection addressed
+- **Data-driven content**: Claims supported by research
+- **Visual integration**: Reference all generated figures
+- **Professional tone**: Consulting-style writing
+- **No token constraints**: Write fully, don't abbreviate
+
+**Writing Guidelines:**
+- Use active voice where possible
+- Lead with insights, support with data
+- Use numbered lists for recommendations
+- Include data sources for all statistics
+- Create smooth transitions between sections
+
+### Phase 5: Compilation & Review
+
+**Step 9: Compile LaTeX**
+
+```bash
+cd writing_outputs/[project_folder]/drafts/
+xelatex v1_market_report.tex
+bibtex v1_market_report
+xelatex v1_market_report.tex
+xelatex v1_market_report.tex
+```
+
+**Step 10: Quality Review**
+
+Verify the report meets quality standards:
+
+- [ ] Total page count is 50+ pages
+- [ ] All essential visuals (5-6 core + any additional) are included and render correctly
+- [ ] Executive summary captures key findings
+- [ ] All data points have sources cited
+- [ ] Analysis frameworks are properly applied
+- [ ] Recommendations are actionable and prioritized
+- [ ] No orphaned figures or tables
+- [ ] Table of contents, list of figures, list of tables are accurate
+- [ ] Bibliography is complete
+- [ ] PDF renders without errors
+
+**Step 11: Peer Review**
+
+Use the peer-review skill to evaluate the report:
+- Assess comprehensiveness
+- Verify data accuracy
+- Check logical flow
+- Evaluate recommendation quality
+
+---
+
+## Quality Standards
+
+### Page Count Targets
+
+| Section | Minimum Pages | Target Pages |
+|---------|---------------|--------------|
+| Front Matter | 4 | 5 |
+| Market Overview | 4 | 5 |
+| Market Size & Growth | 5 | 7 |
+| Industry Drivers | 4 | 6 |
+| Competitive Landscape | 5 | 7 |
+| Customer Analysis | 3 | 5 |
+| Technology Landscape | 3 | 5 |
+| Regulatory Environment | 2 | 4 |
+| Risk Analysis | 2 | 4 |
+| Strategic Recommendations | 3 | 5 |
+| Implementation Roadmap | 2 | 4 |
+| Investment Thesis | 2 | 4 |
+| Back Matter | 4 | 5 |
+| **TOTAL** | **43** | **66** |
+
+### Visual Quality Requirements
+
+- **Resolution**: All images at 300 DPI minimum
+- **Format**: PNG for raster, PDF for vector
+- **Accessibility**: Colorblind-friendly palettes
+- **Consistency**: Same color scheme throughout
+- **Labeling**: All axes, legends, and data points labeled
+- **Source Attribution**: Sources cited in figure captions
+
+### Data Quality Requirements
+
+- **Currency**: Data no older than 2 years (prefer current year)
+- **Sourcing**: All statistics attributed to specific sources
+- **Validation**: Cross-reference multiple sources when possible
+- **Assumptions**: All projections state underlying assumptions
+- **Limitations**: Acknowledge data limitations and gaps
+
+### Writing Quality Requirements
+
+- **Objectivity**: Present balanced analysis, acknowledge uncertainties
+- **Clarity**: Avoid jargon, define technical terms
+- **Precision**: Use specific numbers over vague qualifiers
+- **Structure**: Clear headings, logical flow, smooth transitions
+- **Actionability**: Recommendations are specific and implementable
+
+---
+
+## LaTeX Formatting
+
+### Using the Style Package
+
+The `market_research.sty` package provides professional formatting. Include it in your document:
+
+```latex
+\documentclass[11pt,letterpaper]{report}
+\usepackage{market_research}
+```
+
+### Box Environments
+
+Use colored boxes to highlight key content:
+
+```latex
+% Key insight box (blue)
+\begin{keyinsightbox}[Key Finding]
+The market is projected to grow at 15.3% CAGR through 2030.
+\end{keyinsightbox}
+
+% Market data box (green)
+\begin{marketdatabox}[Market Snapshot]
+\begin{itemize}
+ \item Market Size (2024): \$45.2B
+ \item Projected Size (2030): \$98.7B
+ \item CAGR: 15.3%
+\end{itemize}
+\end{marketdatabox}
+
+% Risk box (orange/warning)
+\begin{riskbox}[Critical Risk]
+Regulatory changes could impact 40% of market participants.
+\end{riskbox}
+
+% Recommendation box (purple)
+\begin{recommendationbox}[Strategic Recommendation]
+Prioritize market entry in the Asia-Pacific region.
+\end{recommendationbox}
+
+% Callout box (gray)
+\begin{calloutbox}[Definition]
+TAM (Total Addressable Market) represents the total revenue opportunity.
+\end{calloutbox}
+```
+
+### Figure Formatting
+
+```latex
+\begin{figure}[htbp]
+\centering
+\includegraphics[width=0.9\textwidth]{../figures/market_growth.png}
+\caption{Market Growth Trajectory (2020-2030). Source: Industry analysis, company data.}
+\label{fig:market_growth}
+\end{figure}
+```
+
+### Table Formatting
+
+```latex
+\begin{table}[htbp]
+\centering
+\caption{Market Size by Region (2024)}
+\begin{tabular}{@{}lrrr@{}}
+\toprule
+\textbf{Region} & \textbf{Size (USD)} & \textbf{Share} & \textbf{CAGR} \\
+\midrule
+North America & \$18.2B & 40.3\% & 12.5\% \\
+\rowcolor{tablealt} Europe & \$12.1B & 26.8\% & 14.2\% \\
+Asia-Pacific & \$10.5B & 23.2\% & 18.7\% \\
+\rowcolor{tablealt} Rest of World & \$4.4B & 9.7\% & 11.3\% \\
+\midrule
+\textbf{Total} & \textbf{\$45.2B} & \textbf{100\%} & \textbf{15.3\%} \\
+\bottomrule
+\end{tabular}
+\label{tab:market_by_region}
+\end{table}
+```
+
+For complete formatting reference, see `assets/FORMATTING_GUIDE.md`.
+
+---
+
+## Integration with Other Skills
+
+This skill works synergistically with:
+
+- **research-lookup**: Essential for gathering market data, statistics, and competitive intelligence
+- **scientific-schematics**: Generate all diagrams, charts, and visualizations
+- **generate-image**: Create infographics and conceptual illustrations
+- **peer-review**: Evaluate report quality and completeness
+- **citation-management**: Manage BibTeX references
+
+---
+
+## Example Prompts
+
+### Market Overview Section
+
+```
+Write a comprehensive market overview section for the [Electric Vehicle Charging Infrastructure] market. Include:
+- Clear market definition and scope
+- Industry ecosystem with key stakeholders
+- Value chain analysis
+- Historical evolution of the market
+- Current market dynamics
+
+Generate 2 supporting visuals using scientific-schematics.
+```
+
+### Competitive Landscape Section
+
+```
+Analyze the competitive landscape for the [Cloud Computing] market. Include:
+- Porter's Five Forces analysis with High/Medium/Low ratings
+- Top 10 competitors with market share
+- Competitive positioning matrix
+- Strategic group mapping
+- Barriers to entry analysis
+
+Generate 4 supporting visuals including Porter's Five Forces diagram and positioning matrix.
+```
+
+### Strategic Recommendations Section
+
+```
+Develop strategic recommendations for entering the [Renewable Energy Storage] market. Include:
+- 5-7 prioritized recommendations
+- Opportunity sizing for each
+- Implementation considerations
+- Risk factors and mitigations
+- Success criteria
+
+Generate 3 supporting visuals including opportunity matrix and priority framework.
+```
+
+---
+
+## Checklist: 50+ Page Validation
+
+Before finalizing the report, verify:
+
+### Structure Completeness
+- [ ] Cover page with hero visual
+- [ ] Table of contents (auto-generated)
+- [ ] List of figures (auto-generated)
+- [ ] List of tables (auto-generated)
+- [ ] Executive summary (2-3 pages)
+- [ ] All 11 core chapters present
+- [ ] Appendix A: Methodology
+- [ ] Appendix B: Data tables
+- [ ] Appendix C: Company profiles
+- [ ] References/Bibliography
+
+### Visual Completeness (Core 5-6)
+- [ ] Market growth trajectory chart (Priority 1)
+- [ ] TAM/SAM/SOM diagram (Priority 2)
+- [ ] Porter's Five Forces (Priority 3)
+- [ ] Competitive positioning matrix (Priority 4)
+- [ ] Risk heatmap (Priority 5)
+- [ ] Executive summary infographic (Priority 6, optional)
+
+### Additional Visuals (Generate as Needed)
+- [ ] Market ecosystem diagram
+- [ ] Regional breakdown chart
+- [ ] Segment growth chart
+- [ ] Industry trends/PESTLE diagram
+- [ ] Market share chart
+- [ ] Customer segmentation chart
+- [ ] Technology roadmap
+- [ ] Regulatory timeline
+- [ ] Opportunity matrix
+- [ ] Implementation timeline
+- [ ] Financial projections chart
+- [ ] Other section-specific visuals
+
+### Content Quality
+- [ ] All statistics have sources
+- [ ] Projections include assumptions
+- [ ] Frameworks properly applied
+- [ ] Recommendations are actionable
+- [ ] Writing is professional quality
+- [ ] No placeholder or incomplete sections
+
+### Technical Quality
+- [ ] PDF compiles without errors
+- [ ] All figures render correctly
+- [ ] Cross-references work
+- [ ] Bibliography complete
+- [ ] Page count exceeds 50
+
+---
+
+## Resources
+
+### Reference Files
+
+Load these files for detailed guidance:
+
+- **`references/report_structure_guide.md`**: Detailed section-by-section content requirements
+- **`references/visual_generation_guide.md`**: Complete prompts for generating all visual types
+- **`references/data_analysis_patterns.md`**: Templates for Porter's, PESTLE, SWOT, etc.
+
+### Assets
+
+- **`assets/market_research.sty`**: LaTeX style package
+- **`assets/market_report_template.tex`**: Complete LaTeX template
+- **`assets/FORMATTING_GUIDE.md`**: Quick reference for box environments and styling
+
+### Scripts
+
+- **`scripts/generate_market_visuals.py`**: Batch generate all report visuals
+
+---
+
+## Troubleshooting
+
+### Common Issues
+
+**Problem**: Report is under 50 pages
+- **Solution**: Expand data tables in appendices, add more detailed company profiles, include additional regional breakdowns
+
+**Problem**: Visuals not rendering
+- **Solution**: Check file paths in LaTeX, ensure images are in figures/ folder, verify file extensions
+
+**Problem**: Bibliography missing entries
+- **Solution**: Run bibtex after first xelatex pass, check .bib file for syntax errors
+
+**Problem**: Table/figure overflow
+- **Solution**: Use `\resizebox` or `adjustbox` package, reduce image width percentage
+
+**Problem**: Poor visual quality from generation
+- **Solution**: Use `--doc-type report` flag, increase iterations with `--iterations 5`
+
+---
+
+Use this skill to create comprehensive, visually-rich market research reports that rival top consulting firm deliverables. The combination of deep research, structured frameworks, and extensive visualization produces documents that inform strategic decisions and demonstrate analytical rigor.
diff --git a/scientific-skills/market-research-reports/assets/FORMATTING_GUIDE.md b/scientific-skills/market-research-reports/assets/FORMATTING_GUIDE.md
new file mode 100644
index 0000000..09a1da4
--- /dev/null
+++ b/scientific-skills/market-research-reports/assets/FORMATTING_GUIDE.md
@@ -0,0 +1,428 @@
+# Market Research Report Formatting Guide
+
+Quick reference for using the `market_research.sty` style package.
+
+## Color Palette
+
+### Primary Colors
+| Color Name | RGB | Hex | Usage |
+|------------|-----|-----|-------|
+| `primaryblue` | (0, 51, 102) | `#003366` | Headers, titles, links |
+| `secondaryblue` | (51, 102, 153) | `#336699` | Subsections, secondary elements |
+| `lightblue` | (173, 216, 230) | `#ADD8E6` | Key insight box backgrounds |
+| `accentblue` | (0, 120, 215) | `#0078D7` | Accent highlights, opportunity boxes |
+
+### Secondary Colors
+| Color Name | RGB | Hex | Usage |
+|------------|-----|-----|-------|
+| `accentgreen` | (0, 128, 96) | `#008060` | Market data boxes, positive indicators |
+| `lightgreen` | (200, 230, 201) | `#C8E6C9` | Market data box backgrounds |
+| `warningorange` | (255, 140, 0) | `#FF8C00` | Risk boxes, warnings |
+| `alertred` | (198, 40, 40) | `#C62828` | Critical risks |
+| `recommendpurple` | (103, 58, 183) | `#673AB7` | Recommendation boxes |
+
+### Neutral Colors
+| Color Name | RGB | Hex | Usage |
+|------------|-----|-----|-------|
+| `darkgray` | (66, 66, 66) | `#424242` | Body text |
+| `mediumgray` | (117, 117, 117) | `#757575` | Secondary text |
+| `lightgray` | (240, 240, 240) | `#F0F0F0` | Backgrounds, callout boxes |
+| `tablealt` | (245, 247, 250) | `#F5F7FA` | Alternating table rows |
+
+---
+
+## Box Environments
+
+### Key Insight Box (Blue)
+For major findings, insights, and important discoveries.
+
+```latex
+\begin{keyinsightbox}[Custom Title]
+The market is projected to grow at 15.3% CAGR through 2030, driven by
+increasing enterprise adoption and favorable regulatory conditions.
+\end{keyinsightbox}
+```
+
+### Market Data Box (Green)
+For market statistics, metrics, and data highlights.
+
+```latex
+\begin{marketdatabox}[Market Snapshot]
+\begin{itemize}
+ \item \textbf{Market Size (2024):} \marketsize{45.2 billion}
+ \item \textbf{Projected Size (2030):} \marketsize{98.7 billion}
+ \item \textbf{CAGR:} \growthrate{15.3}
+\end{itemize}
+\end{marketdatabox}
+```
+
+### Risk Box (Orange/Warning)
+For risk factors, warnings, and cautions.
+
+```latex
+\begin{riskbox}[Market Risk]
+Regulatory changes in the European Union could impact 40% of market
+participants within the next 18 months.
+\end{riskbox}
+```
+
+### Critical Risk Box (Red)
+For high-severity or critical risks.
+
+```latex
+\begin{criticalriskbox}[Critical: Supply Chain Disruption]
+A major supply chain disruption could result in 6-12 month delays
+and 30% cost increases.
+\end{criticalriskbox}
+```
+
+### Recommendation Box (Purple)
+For strategic recommendations and action items.
+
+```latex
+\begin{recommendationbox}[Strategic Recommendation]
+\begin{enumerate}
+ \item Prioritize market entry in Asia-Pacific region
+ \item Develop strategic partnerships with local distributors
+ \item Invest in localization of product offerings
+\end{enumerate}
+\end{recommendationbox}
+```
+
+### Callout Box (Gray)
+For definitions, notes, and supplementary information.
+
+```latex
+\begin{calloutbox}[Definition: TAM]
+Total Addressable Market (TAM) represents the total revenue opportunity
+available if 100% market share was achieved.
+\end{calloutbox}
+```
+
+### Executive Summary Box
+Special styling for executive summary highlights.
+
+```latex
+\begin{executivesummarybox}[Executive Summary]
+Key findings and highlights of the report...
+\end{executivesummarybox}
+```
+
+### Opportunity Box (Teal/Accent Blue)
+For opportunities and positive findings.
+
+```latex
+\begin{opportunitybox}[Growth Opportunity]
+The Asia-Pacific market represents a \$15 billion opportunity
+growing at 22% CAGR.
+\end{opportunitybox}
+```
+
+### Framework Boxes
+For strategic analysis frameworks.
+
+```latex
+% SWOT Analysis
+\begin{swotbox}[SWOT Analysis Summary]
+Content...
+\end{swotbox}
+
+% Porter's Five Forces
+\begin{porterbox}[Porter's Five Forces Analysis]
+Content...
+\end{porterbox}
+```
+
+---
+
+## Pull Quotes
+
+For highlighting important statistics or quotes.
+
+```latex
+\begin{pullquote}
+"The convergence of AI and healthcare represents a \$199 billion
+opportunity by 2034."
+\end{pullquote}
+```
+
+---
+
+## Stat Boxes
+
+For highlighting key statistics (use in rows of 3).
+
+```latex
+\begin{center}
+\statbox{\$45.2B}{Market Size 2024}
+\statbox{15.3\%}{CAGR 2024-2030}
+\statbox{23\%}{Market Leader Share}
+\end{center}
+```
+
+---
+
+## Custom Commands
+
+### Highlighting Text
+```latex
+\highlight{Important text} % Blue bold
+```
+
+### Market Size Formatting
+```latex
+\marketsize{45.2 billion} % Outputs: $45.2 billion in green
+```
+
+### Growth Rate Formatting
+```latex
+\growthrate{15.3} % Outputs: 15.3% in green
+```
+
+### Risk Indicators
+```latex
+\riskhigh{} % Outputs: HIGH in red
+\riskmedium{} % Outputs: MEDIUM in orange
+\risklow{} % Outputs: LOW in green
+```
+
+### Rating Stars (1-5)
+```latex
+\rating{4} % Outputs: ★★★★☆
+```
+
+### Trend Indicators
+```latex
+\trendup{} % Green up triangle
+\trenddown{} % Red down triangle
+\trendflat{} % Gray right arrow
+```
+
+---
+
+## Table Formatting
+
+### Standard Table with Alternating Rows
+```latex
+\begin{table}[htbp]
+\centering
+\caption{Market Size by Region}
+\begin{tabular}{@{}lrrr@{}}
+\toprule
+\textbf{Region} & \textbf{Size} & \textbf{Share} & \textbf{CAGR} \\
+\midrule
+North America & \$18.2B & 40.3\% & 12.5\% \\
+\rowcolor{tablealt} Europe & \$12.1B & 26.8\% & 14.2\% \\
+Asia-Pacific & \$10.5B & 23.2\% & 18.7\% \\
+\rowcolor{tablealt} Rest of World & \$4.4B & 9.7\% & 11.3\% \\
+\midrule
+\textbf{Total} & \textbf{\$45.2B} & \textbf{100\%} & \textbf{15.3\%} \\
+\bottomrule
+\end{tabular}
+\label{tab:regional}
+\end{table}
+```
+
+### Table with Trend Indicators
+```latex
+\begin{tabular}{@{}lrrl@{}}
+\toprule
+\textbf{Company} & \textbf{Revenue} & \textbf{Share} & \textbf{Trend} \\
+\midrule
+Company A & \$5.2B & 15.3\% & \trendup{} +12\% \\
+Company B & \$4.8B & 14.1\% & \trenddown{} -3\% \\
+Company C & \$4.2B & 12.4\% & \trendflat{} +1\% \\
+\bottomrule
+\end{tabular}
+```
+
+---
+
+## Figure Formatting
+
+### Standard Figure
+```latex
+\begin{figure}[htbp]
+\centering
+\includegraphics[width=0.9\textwidth]{../figures/market_growth.png}
+\caption{Market Growth Trajectory (2020-2030)}
+\label{fig:growth}
+\end{figure}
+```
+
+### Figure with Source Attribution
+```latex
+\begin{figure}[htbp]
+\centering
+\includegraphics[width=0.85\textwidth]{../figures/market_share.png}
+\caption{Market Share Distribution (2024)}
+\figuresource{Company annual reports, industry analysis}
+\label{fig:market_share}
+\end{figure}
+```
+
+---
+
+## List Formatting
+
+### Bullet Lists
+```latex
+\begin{itemize}
+ \item First item with automatic blue bullet
+ \item Second item
+ \item Third item
+\end{itemize}
+```
+
+### Numbered Lists
+```latex
+\begin{enumerate}
+ \item First item with blue number
+ \item Second item
+ \item Third item
+\end{enumerate}
+```
+
+### Nested Lists
+```latex
+\begin{itemize}
+ \item Main point
+ \begin{itemize}
+ \item Sub-point A
+ \item Sub-point B
+ \end{itemize}
+ \item Another main point
+\end{itemize}
+```
+
+---
+
+## Title Page
+
+### Using the Custom Title Command
+```latex
+\makemarketreporttitle
+ {Market Title} % Report title
+ {Subtitle Here} % Subtitle
+ {../figures/cover.png} % Hero image (leave empty for no image)
+ {January 2025} % Date
+ {Market Intelligence Team} % Author/prepared by
+```
+
+### Manual Title Page
+See the template for full manual title page code.
+
+---
+
+## Appendix Sections
+
+```latex
+\appendix
+
+\chapter{Methodology}
+
+\appendixsection{Data Sources}
+Content that appears in table of contents...
+```
+
+---
+
+## Common Patterns
+
+### Market Snapshot Section
+```latex
+\begin{marketdatabox}[Market Snapshot]
+\begin{itemize}
+ \item \textbf{Current Market Size:} \marketsize{45.2 billion}
+ \item \textbf{Projected Size (2030):} \marketsize{98.7 billion}
+ \item \textbf{CAGR:} \growthrate{15.3}
+ \item \textbf{Largest Segment:} Enterprise (42\% share)
+ \item \textbf{Fastest Growing Region:} APAC (\growthrate{22.1} CAGR)
+\end{itemize}
+\end{marketdatabox}
+```
+
+### Risk Register Summary
+```latex
+\begin{table}[htbp]
+\centering
+\caption{Risk Assessment Summary}
+\begin{tabular}{@{}llccl@{}}
+\toprule
+\textbf{Risk} & \textbf{Category} & \textbf{Prob.} & \textbf{Impact} & \textbf{Rating} \\
+\midrule
+Market disruption & Market & High & High & \riskhigh{} \\
+\rowcolor{tablealt} Regulatory change & Regulatory & Med & High & \riskhigh{} \\
+New entrant & Competitive & Med & Med & \riskmedium{} \\
+\rowcolor{tablealt} Tech obsolescence & Technology & Low & High & \riskmedium{} \\
+Currency fluctuation & Financial & Med & Low & \risklow{} \\
+\bottomrule
+\end{tabular}
+\end{table}
+```
+
+### Competitive Comparison Table
+```latex
+\begin{table}[htbp]
+\centering
+\caption{Competitive Comparison}
+\begin{tabular}{@{}lccccc@{}}
+\toprule
+\textbf{Factor} & \textbf{Co. A} & \textbf{Co. B} & \textbf{Co. C} & \textbf{Co. D} \\
+\midrule
+Market Share & \rating{5} & \rating{4} & \rating{3} & \rating{2} \\
+\rowcolor{tablealt} Product Quality & \rating{4} & \rating{5} & \rating{3} & \rating{4} \\
+Price Competitiveness & \rating{3} & \rating{3} & \rating{5} & \rating{4} \\
+\rowcolor{tablealt} Innovation & \rating{5} & \rating{4} & \rating{2} & \rating{3} \\
+Customer Service & \rating{4} & \rating{4} & \rating{4} & \rating{5} \\
+\bottomrule
+\end{tabular}
+\end{table}
+```
+
+---
+
+## Troubleshooting
+
+### Box Overflow
+If box content overflows the page, break into multiple boxes or use page breaks:
+```latex
+\newpage
+\begin{keyinsightbox}[Continued...]
+```
+
+### Figure Placement
+Use `[htbp]` for flexible placement, or `[H]` (requires `float` package) for exact placement:
+```latex
+\begin{figure}[H] % Requires \usepackage{float}
+```
+
+### Table Too Wide
+Use `\resizebox` or `adjustbox`:
+```latex
+\resizebox{\textwidth}{!}{
+\begin{tabular}{...}
+...
+\end{tabular}
+}
+```
+
+### Color Not Appearing
+Ensure `xcolor` package is loaded with `[table]` option (already included in style file).
+
+---
+
+## Compilation
+
+Compile with XeLaTeX for best results:
+```bash
+xelatex report.tex
+bibtex report
+xelatex report.tex
+xelatex report.tex
+```
+
+Or use latexmk:
+```bash
+latexmk -xelatex report.tex
+```
diff --git a/scientific-skills/market-research-reports/assets/market_report_template.tex b/scientific-skills/market-research-reports/assets/market_report_template.tex
new file mode 100644
index 0000000..244264b
--- /dev/null
+++ b/scientific-skills/market-research-reports/assets/market_report_template.tex
@@ -0,0 +1,1380 @@
+% !TEX program = xelatex
+% Market Research Report Template
+% Professional formatting for 50+ page comprehensive market reports
+% Use with market_research.sty style package
+
+\documentclass[11pt,letterpaper]{report}
+\usepackage{market_research}
+
+% ============================================================================
+% DOCUMENT METADATA - CUSTOMIZE THESE
+% ============================================================================
+\newcommand{\reporttitle}{[MARKET NAME]}
+\newcommand{\reportsubtitle}{Comprehensive Market Analysis Report}
+\newcommand{\reportdate}{\today}
+\newcommand{\reportauthor}{Market Intelligence Division}
+\newcommand{\reportclassification}{Confidential}
+
+% ============================================================================
+% PDF METADATA
+% ============================================================================
+\hypersetup{
+ pdftitle={\reporttitle{} - \reportsubtitle{}},
+ pdfauthor={\reportauthor{}},
+ pdfsubject={Market Research Report},
+ pdfkeywords={market research, market analysis, competitive landscape, strategic analysis}
+}
+
+% ============================================================================
+% DOCUMENT START
+% ============================================================================
+\begin{document}
+
+% ============================================================================
+% TITLE PAGE
+% ============================================================================
+% To use a hero image, replace the empty braces with the path:
+% \makemarketreporttitle{\reporttitle}{\reportsubtitle}{../figures/cover_image.png}{\reportdate}{\reportauthor}
+
+\begin{titlepage}
+\centering
+\vspace*{2cm}
+
+{\Huge\bfseries\color{primaryblue} \reporttitle\\[0.5cm]}
+{\LARGE\bfseries \reportsubtitle\\[1.5cm]}
+
+% VISUAL: Generate hero/cover image
+% python skills/generate-image/scripts/generate_image.py "Professional executive summary infographic for [MARKET] market research report, showing key metrics in modern data visualization style, blue and green color scheme, clean minimalist design" --output figures/cover_image.png
+% Uncomment below when image is generated:
+% \includegraphics[width=\textwidth]{../figures/cover_image.png}\\[1.5cm]
+
+\vspace{4cm}
+
+{\Large\bfseries Comprehensive Market Research Report\\[0.5cm]}
+{\large Strategic Intelligence for Business Decision-Making\\[3cm]}
+
+{\large
+\textbf{Date:} \reportdate\\[0.3cm]
+\textbf{Prepared By:} \reportauthor\\[0.3cm]
+\textbf{Classification:} \reportclassification\\[0.3cm]
+\textbf{Report Type:} Full Market Analysis
+}
+
+\vfill
+
+{\footnotesize
+\textit{This report contains market intelligence and strategic analysis based on publicly available data and proprietary research. All sources are cited and independently verifiable.}
+}
+
+\end{titlepage}
+
+% ============================================================================
+% FRONT MATTER
+% ============================================================================
+\pagenumbering{roman}
+
+% Table of Contents
+\tableofcontents
+\newpage
+
+% List of Figures
+\listoffigures
+\newpage
+
+% List of Tables
+\listoftables
+\newpage
+
+% ============================================================================
+% MAIN CONTENT
+% ============================================================================
+\pagenumbering{arabic}
+
+% ============================================================================
+% EXECUTIVE SUMMARY (2-3 pages)
+% ============================================================================
+\chapter{Executive Summary}
+
+\section{Report Overview}
+
+This comprehensive market analysis examines the \reporttitle{} market, providing strategic intelligence for investors, executives, and strategic planners. The report synthesizes data from authoritative sources including market research firms, regulatory agencies, industry associations, and enterprise surveys.
+
+% VISUAL: Executive summary infographic
+% python skills/scientific-schematics/scripts/generate_schematic.py "Executive summary infographic showing 4 key metrics: Market Size $XX.XB (2024), CAGR XX.X%, Top 3 Players, and Key Trend. Use blue boxes with white text, professional layout" -o figures/exec_summary_infographic.png --doc-type report
+
+\subsection{Market Snapshot}
+
+\begin{marketdatabox}[Market Snapshot: \reporttitle{}]
+\begin{itemize}[leftmargin=*]
+ \item \textbf{Current Market Size (2024):} \marketsize{X.XX billion}
+ \item \textbf{Projected Market Size (2034):} \marketsize{XX.XX billion}
+ \item \textbf{Compound Annual Growth Rate (CAGR):} \growthrate{XX.X}
+ \item \textbf{Growth Multiple:} Xx increase over 10 years
+ \item \textbf{Largest Segment:} [Segment Name] (XX\% market share)
+ \item \textbf{Fastest Growing Region:} [Region] (\growthrate{XX.X} CAGR)
+ \item \textbf{Current Enterprise Adoption:} XX\%
+\end{itemize}
+\end{marketdatabox}
+
+\subsection{Investment Thesis}
+
+The convergence of multiple market catalysts creates a compelling opportunity for investment and strategic action in the \reporttitle{} market:
+
+\begin{keyinsightbox}[Key Investment Drivers]
+\begin{enumerate}
+ \item \textbf{[Driver 1]:} [Brief explanation of why this driver creates opportunity]
+ \item \textbf{[Driver 2]:} [Brief explanation]
+ \item \textbf{[Driver 3]:} [Brief explanation]
+ \item \textbf{[Driver 4]:} [Brief explanation]
+\end{enumerate}
+\end{keyinsightbox}
+
+\subsection{Key Findings}
+
+\paragraph{Market Dynamics}
+[Summarize the most important findings about market size, growth, and dynamics. Include 3-5 key statistics with sources.]
+
+\paragraph{Competitive Landscape}
+[Summarize competitive dynamics, market concentration, and key players. Include market share of top players.]
+
+\paragraph{Growth Drivers}
+[Summarize the primary factors driving market growth and their expected impact.]
+
+\paragraph{Risk Factors}
+[Summarize the key risks that could impact market development.]
+
+\subsection{Strategic Recommendations}
+
+Based on the comprehensive analysis presented in this report, we recommend the following strategic actions:
+
+\begin{recommendationbox}[Top Strategic Recommendations]
+\begin{enumerate}
+ \item \textbf{[Recommendation 1]:} [Action-oriented recommendation with expected outcome]
+ \item \textbf{[Recommendation 2]:} [Action-oriented recommendation with expected outcome]
+ \item \textbf{[Recommendation 3]:} [Action-oriented recommendation with expected outcome]
+ \item \textbf{[Recommendation 4]:} [Action-oriented recommendation with expected outcome]
+ \item \textbf{[Recommendation 5]:} [Action-oriented recommendation with expected outcome]
+\end{enumerate}
+\end{recommendationbox}
+
+% ============================================================================
+% CHAPTER 1: MARKET OVERVIEW & DEFINITION (4-5 pages)
+% ============================================================================
+\chapter{Market Overview \& Definition}
+
+\section{Market Definition}
+
+[Provide a clear, comprehensive definition of the market being analyzed. Include:
+- What products/services are included
+- What is explicitly excluded
+- How this market relates to adjacent markets
+- Industry classification codes if applicable (NAICS, SIC)]
+
+\begin{calloutbox}[Market Definition]
+The \reporttitle{} market encompasses [comprehensive definition]. This includes [included elements] and excludes [excluded elements].
+\end{calloutbox}
+
+\subsection{Scope and Boundaries}
+
+\paragraph{Geographic Scope}
+[Define the geographic boundaries of the analysis - global, regional, or specific countries.]
+
+\paragraph{Product/Service Scope}
+[Define what products and services are included in the market definition.]
+
+\paragraph{Time Horizon}
+[Specify the historical period analyzed and the forecast period.]
+
+\subsection{Market Classification}
+
+[Provide detailed market classification and taxonomy, including:
+- Market segments
+- Sub-segments
+- Categories]
+
+\section{Industry Ecosystem}
+
+% VISUAL: Industry ecosystem diagram
+% python skills/scientific-schematics/scripts/generate_schematic.py "Industry ecosystem diagram showing value chain from [Raw Materials/Inputs] on left through [Manufacturing/Processing] through [Distribution] to [End Users] on right. Include key players at each stage. Use blue boxes connected by arrows" -o figures/industry_ecosystem.png --doc-type report
+
+[Describe the industry ecosystem and value chain, including:
+- Key stakeholders and their roles
+- Relationships between stakeholders
+- Value creation at each stage
+- Information and money flows]
+
+\begin{figure}[htbp]
+\centering
+% \includegraphics[width=0.95\textwidth]{../figures/industry_ecosystem.png}
+\caption{Industry Ecosystem and Value Chain}
+\label{fig:ecosystem}
+\end{figure}
+
+\subsection{Key Stakeholders}
+
+[Describe each category of stakeholder:]
+
+\paragraph{Suppliers/Vendors}
+[Description of upstream suppliers and their role.]
+
+\paragraph{Manufacturers/Service Providers}
+[Description of core market participants.]
+
+\paragraph{Distributors/Channels}
+[Description of distribution and go-to-market channels.]
+
+\paragraph{End Users/Customers}
+[Description of customer segments and their needs.]
+
+\paragraph{Regulators and Industry Bodies}
+[Description of regulatory environment and industry associations.]
+
+\section{Market Structure}
+
+% VISUAL: Market structure diagram
+% python skills/scientific-schematics/scripts/generate_schematic.py "Market structure diagram showing industry layers: [Core Market] in center, surrounded by [Adjacent Markets], with [Enabling Technologies] as foundation and [Regulatory Framework] as overlay. Use concentric rectangles" -o figures/market_structure.png --doc-type report
+
+[Describe the structure of the market:]
+
+\subsection{Market Concentration}
+
+[Analyze market concentration using metrics like:
+- Herfindahl-Hirschman Index (HHI)
+- CR4/CR8 concentration ratios
+- Market fragmentation assessment]
+
+\subsection{Industry Lifecycle Stage}
+
+[Identify where the market is in its lifecycle:
+- Introduction
+- Growth
+- Maturity
+- Decline]
+
+\section{Historical Context}
+
+[Provide historical background on the market:
+- When did the market emerge?
+- Key milestones in market development
+- Major industry shifts and disruptions
+- How has the market evolved over time?]
+
+% ============================================================================
+% CHAPTER 2: MARKET SIZE & GROWTH ANALYSIS (6-8 pages)
+% ============================================================================
+\chapter{Market Size \& Growth Analysis}
+
+\section{Total Addressable Market (TAM)}
+
+The Total Addressable Market represents the total revenue opportunity available if 100\% market share was achieved. Based on comprehensive analysis from multiple research sources:
+
+% VISUAL: Market growth trajectory
+% python skills/scientific-schematics/scripts/generate_schematic.py "Bar chart showing market growth from 2020 to 2034. Historical bars (2020-2024) in dark blue, projected bars (2025-2034) in light blue. Y-axis in billions USD, X-axis showing years. Include CAGR label. Title: [MARKET] Market Growth Trajectory" -o figures/market_growth_trajectory.png --doc-type report
+
+\begin{table}[htbp]
+\centering
+\caption{Global \reporttitle{} Market Projections (2024-2034)}
+\begin{tabular}{@{}lrrr@{}}
+\toprule
+\textbf{Year} & \textbf{Market Size (USD)} & \textbf{YoY Growth} & \textbf{CAGR} \\
+\midrule
+2024 & \$X.XX B & -- & -- \\
+\rowcolor{tablealt} 2025 & \$X.XX B & XX.X\% & XX.X\% \\
+2026 & \$X.XX B & XX.X\% & XX.X\% \\
+\rowcolor{tablealt} 2027 & \$X.XX B & XX.X\% & XX.X\% \\
+2028 & \$X.XX B & XX.X\% & XX.X\% \\
+\rowcolor{tablealt} 2029 & \$X.XX B & XX.X\% & XX.X\% \\
+2030 & \$X.XX B & XX.X\% & XX.X\% \\
+\rowcolor{tablealt} 2031 & \$X.XX B & XX.X\% & XX.X\% \\
+2032 & \$X.XX B & XX.X\% & XX.X\% \\
+\rowcolor{tablealt} 2033 & \$X.XX B & XX.X\% & XX.X\% \\
+2034 & \$X.XX B & XX.X\% & XX.X\% \\
+\bottomrule
+\end{tabular}
+\label{tab:tam_projections}
+\end{table}
+
+\textbf{Source:} [Primary research source, year]
+
+\begin{figure}[htbp]
+\centering
+% \includegraphics[width=0.9\textwidth]{../figures/market_growth_trajectory.png}
+\caption{Market Growth Trajectory (2020-2034)}
+\label{fig:market_growth}
+\end{figure}
+
+\subsection{Historical Growth Analysis}
+
+[Analyze historical market performance over the past 5-10 years:
+- Historical CAGR
+- Key growth periods and drivers
+- Impact of major events (recessions, disruptions, etc.)
+- Comparison to overall economic growth]
+
+\subsection{Growth Projections Methodology}
+
+[Explain the methodology behind growth projections:
+- Key assumptions
+- Data sources
+- Modeling approach
+- Confidence intervals]
+
+\section{Serviceable Addressable Market (SAM)}
+
+The Serviceable Addressable Market represents the portion of TAM that can be served given current product offerings, geographic presence, and regulatory constraints.
+
+% VISUAL: TAM/SAM/SOM diagram
+% python skills/scientific-schematics/scripts/generate_schematic.py "TAM SAM SOM concentric circle diagram. Outer circle: TAM $XXB (Total Addressable Market). Middle circle: SAM $XXB (Serviceable Addressable Market). Inner circle: SOM $XXB (Serviceable Obtainable Market). Labels with arrows pointing to each. Professional blue color scheme" -o figures/tam_sam_som.png --doc-type report
+
+\begin{figure}[htbp]
+\centering
+% \includegraphics[width=0.8\textwidth]{../figures/tam_sam_som.png}
+\caption{TAM/SAM/SOM Market Opportunity Breakdown}
+\label{fig:tam_sam_som}
+\end{figure}
+
+\begin{table}[htbp]
+\centering
+\caption{Market Segments Within SAM (2024 vs 2034)}
+\begin{tabular}{@{}lrrrr@{}}
+\toprule
+\textbf{Segment} & \textbf{2024 Value} & \textbf{2034 Value} & \textbf{CAGR} & \textbf{Share} \\
+\midrule
+Segment A & \$X.XX B & \$XX.XX B & XX.X\% & XX\% \\
+\rowcolor{tablealt} Segment B & \$X.XX B & \$XX.XX B & XX.X\% & XX\% \\
+Segment C & \$X.XX B & \$XX.XX B & XX.X\% & XX\% \\
+\rowcolor{tablealt} Segment D & \$X.XX B & \$XX.XX B & XX.X\% & XX\% \\
+Segment E & \$X.XX B & \$XX.XX B & XX.X\% & XX\% \\
+\midrule
+\textbf{Total SAM} & \textbf{\$X.XX B} & \textbf{\$XX.XX B} & \textbf{XX.X\%} & \textbf{100\%} \\
+\bottomrule
+\end{tabular}
+\label{tab:sam_segments}
+\end{table}
+
+\section{Serviceable Obtainable Market (SOM)}
+
+The Serviceable Obtainable Market represents the realistic market share capture based on competitive dynamics, go-to-market capabilities, and strategic positioning.
+
+\begin{keyinsightbox}[SOM Projections (2034)]
+\textbf{Conservative Scenario (XX\% Market Share):} \marketsize{X.X billion}
+\begin{itemize}
+ \item Assumes competitive market with multiple major players
+ \item Typical XX-XX month enterprise sales cycles
+ \item Focus on [specific segments]
+\end{itemize}
+
+\textbf{Base Case Scenario (XX\% Market Share):} \marketsize{X.X billion}
+\begin{itemize}
+ \item Captures first-mover advantages in key segments
+ \item Strong product-market fit
+ \item Established partnership ecosystem
+\end{itemize}
+
+\textbf{Optimistic Scenario (XX\% Market Share):} \marketsize{X.X billion}
+\begin{itemize}
+ \item Market leadership position
+ \item Platform effects and network advantages
+ \item Proprietary advantages and moats
+\end{itemize}
+\end{keyinsightbox}
+
+\section{Regional Market Analysis}
+
+% VISUAL: Regional breakdown
+% python skills/scientific-schematics/scripts/generate_schematic.py "Pie chart or treemap showing regional market breakdown. North America XX%, Europe XX%, Asia-Pacific XX%, Latin America XX%, Middle East & Africa XX%. Use distinct colors for each region. Include both percentage and dollar values" -o figures/regional_breakdown.png --doc-type report
+
+\begin{figure}[htbp]
+\centering
+% \includegraphics[width=0.8\textwidth]{../figures/regional_breakdown.png}
+\caption{Market Size by Region (2024)}
+\label{fig:regional_breakdown}
+\end{figure}
+
+\begin{table}[htbp]
+\centering
+\caption{Regional Market Size and Growth}
+\begin{tabular}{@{}lrrrr@{}}
+\toprule
+\textbf{Region} & \textbf{2024 Size} & \textbf{Share} & \textbf{CAGR} & \textbf{2034 Size} \\
+\midrule
+North America & \$X.XX B & XX.X\% & XX.X\% & \$XX.XX B \\
+\rowcolor{tablealt} Europe & \$X.XX B & XX.X\% & XX.X\% & \$XX.XX B \\
+Asia-Pacific & \$X.XX B & XX.X\% & XX.X\% & \$XX.XX B \\
+\rowcolor{tablealt} Latin America & \$X.XX B & XX.X\% & XX.X\% & \$XX.XX B \\
+Middle East \& Africa & \$X.XX B & XX.X\% & XX.X\% & \$XX.XX B \\
+\midrule
+\textbf{Global Total} & \textbf{\$X.XX B} & \textbf{100\%} & \textbf{XX.X\%} & \textbf{\$XX.XX B} \\
+\bottomrule
+\end{tabular}
+\label{tab:regional_market}
+\end{table}
+
+\subsection{North America}
+[Detailed analysis of North American market including US and Canada specifics.]
+
+\subsection{Europe}
+[Detailed analysis of European market including key country breakdowns.]
+
+\subsection{Asia-Pacific}
+[Detailed analysis of APAC market with focus on China, Japan, India, and emerging markets.]
+
+\subsection{Rest of World}
+[Analysis of Latin America, Middle East, and Africa markets.]
+
+\section{Segment Analysis}
+
+% VISUAL: Segment growth comparison
+% python skills/scientific-schematics/scripts/generate_schematic.py "Horizontal bar chart comparing segment growth rates. Segments listed on Y-axis, CAGR percentage on X-axis. Bars colored from green (highest growth) to blue (lowest growth). Include data labels on each bar" -o figures/segment_growth.png --doc-type report
+
+\begin{figure}[htbp]
+\centering
+% \includegraphics[width=0.9\textwidth]{../figures/segment_growth.png}
+\caption{Segment Growth Rate Comparison (CAGR 2024-2034)}
+\label{fig:segment_growth}
+\end{figure}
+
+[Provide detailed analysis of each market segment including:
+- Current size and market share
+- Growth trajectory
+- Key drivers for each segment
+- Competitive dynamics within segment]
+
+% ============================================================================
+% CHAPTER 3: INDUSTRY DRIVERS & TRENDS (5-6 pages)
+% ============================================================================
+\chapter{Industry Drivers \& Trends}
+
+\section{Primary Growth Drivers}
+
+[Identify and analyze the key factors driving market growth:]
+
+% VISUAL: Driver impact matrix
+% python skills/scientific-schematics/scripts/generate_schematic.py "2x2 matrix showing market drivers. X-axis: Impact (Low to High). Y-axis: Likelihood (Low to High). Plot 8-10 drivers as circles. Upper-right quadrant labeled 'Critical Drivers', lower-right 'Watch Carefully', upper-left 'Monitor', lower-left 'Lower Priority'. Professional blue and green colors" -o figures/driver_impact_matrix.png --doc-type report
+
+\begin{figure}[htbp]
+\centering
+% \includegraphics[width=0.85\textwidth]{../figures/driver_impact_matrix.png}
+\caption{Market Driver Impact Assessment Matrix}
+\label{fig:driver_matrix}
+\end{figure}
+
+\subsection{Driver 1: [Name]}
+[Detailed analysis of this driver including:
+- How it affects the market
+- Quantified impact
+- Timeline for impact
+- Supporting evidence and data]
+
+\subsection{Driver 2: [Name]}
+[Detailed analysis]
+
+\subsection{Driver 3: [Name]}
+[Detailed analysis]
+
+\subsection{Driver 4: [Name]}
+[Detailed analysis]
+
+\subsection{Driver 5: [Name]}
+[Detailed analysis]
+
+\section{PESTLE Analysis}
+
+% VISUAL: PESTLE diagram
+% python skills/scientific-schematics/scripts/generate_schematic.py "PESTLE analysis diagram with center hexagon labeled 'Market' surrounded by 6 hexagons: Political (red), Economic (blue), Social (green), Technological (orange), Legal (purple), Environmental (teal). Each outer hexagon contains 2-3 bullet points of key factors" -o figures/pestle_analysis.png --doc-type report
+
+\begin{figure}[htbp]
+\centering
+% \includegraphics[width=0.9\textwidth]{../figures/pestle_analysis.png}
+\caption{PESTLE Analysis Framework}
+\label{fig:pestle}
+\end{figure}
+
+\subsection{Political Factors}
+[Analysis of political factors affecting the market:
+- Government policies
+- Political stability
+- Trade policies
+- Tax regulations]
+
+\subsection{Economic Factors}
+[Analysis of economic factors:
+- Economic growth
+- Interest rates
+- Inflation
+- Exchange rates
+- Consumer spending]
+
+\subsection{Social Factors}
+[Analysis of social factors:
+- Demographics
+- Cultural trends
+- Consumer attitudes
+- Workforce trends]
+
+\subsection{Technological Factors}
+[Analysis of technological factors:
+- Technology adoption
+- R\&D activity
+- Automation
+- Digital transformation]
+
+\subsection{Legal Factors}
+[Analysis of legal factors:
+- Industry regulations
+- Compliance requirements
+- Intellectual property
+- Employment laws]
+
+\subsection{Environmental Factors}
+[Analysis of environmental factors:
+- Sustainability requirements
+- Environmental regulations
+- Climate impact
+- Resource availability]
+
+\section{Emerging Trends}
+
+% VISUAL: Trends timeline
+% python skills/scientific-schematics/scripts/generate_schematic.py "Horizontal timeline showing emerging trends from 2024 to 2030. Mark 6-8 trends at different points on timeline with icons and labels. Use different colors for Technology trends (blue), Market trends (green), and Regulatory trends (orange). Include brief descriptions below each trend" -o figures/trends_timeline.png --doc-type report
+
+\begin{figure}[htbp]
+\centering
+% \includegraphics[width=\textwidth]{../figures/trends_timeline.png}
+\caption{Emerging Industry Trends Timeline}
+\label{fig:trends}
+\end{figure}
+
+[Identify and analyze emerging trends that will shape the market:]
+
+\subsection{Trend 1: [Name]}
+[Detailed trend analysis]
+
+\subsection{Trend 2: [Name]}
+[Detailed trend analysis]
+
+\subsection{Trend 3: [Name]}
+[Detailed trend analysis]
+
+\section{Growth Inhibitors}
+
+[Identify factors that could slow market growth:
+- Market barriers
+- Resource constraints
+- Adoption challenges
+- Competitive pressures]
+
+% ============================================================================
+% CHAPTER 4: COMPETITIVE LANDSCAPE (6-8 pages)
+% ============================================================================
+\chapter{Competitive Landscape}
+
+\section{Market Structure Analysis}
+
+[Analyze the competitive structure of the market:]
+
+\subsection{Market Concentration}
+
+[Provide market concentration analysis:
+- Number of competitors
+- Market share distribution
+- Concentration metrics (HHI, CR4)]
+
+\section{Porter's Five Forces Analysis}
+
+% VISUAL: Porter's Five Forces
+% python skills/scientific-schematics/scripts/generate_schematic.py "Porter's Five Forces diagram. Center box labeled 'Competitive Rivalry: [HIGH/MEDIUM/LOW]'. Four boxes around it connected by arrows: 'Threat of New Entrants: [RATING]' (top), 'Bargaining Power of Suppliers: [RATING]' (left), 'Bargaining Power of Buyers: [RATING]' (right), 'Threat of Substitutes: [RATING]' (bottom). Color code by rating: High=red, Medium=orange, Low=green" -o figures/porters_five_forces.png --doc-type report
+
+\begin{figure}[htbp]
+\centering
+% \includegraphics[width=0.85\textwidth]{../figures/porters_five_forces.png}
+\caption{Porter's Five Forces Analysis}
+\label{fig:porter}
+\end{figure}
+
+\begin{porterbox}[Porter's Five Forces Summary]
+\begin{tabular}{@{}ll@{}}
+\textbf{Force} & \textbf{Rating} \\
+\midrule
+Threat of New Entrants & \riskmedium{} \\
+Bargaining Power of Suppliers & \risklow{} \\
+Bargaining Power of Buyers & \riskhigh{} \\
+Threat of Substitutes & \risklow{} \\
+Competitive Rivalry & \riskhigh{} \\
+\end{tabular}
+\end{porterbox}
+
+\subsection{Threat of New Entrants}
+[Detailed analysis of barriers to entry and threat level]
+
+\subsection{Bargaining Power of Suppliers}
+[Detailed analysis of supplier power dynamics]
+
+\subsection{Bargaining Power of Buyers}
+[Detailed analysis of buyer power dynamics]
+
+\subsection{Threat of Substitutes}
+[Detailed analysis of substitute products/services]
+
+\subsection{Competitive Rivalry}
+[Detailed analysis of competitive intensity]
+
+\section{Market Share Analysis}
+
+% VISUAL: Market share chart
+% python skills/scientific-schematics/scripts/generate_schematic.py "Pie chart showing market share of top 10 companies. Company A XX%, Company B XX%, Company C XX%, [etc.], Others XX%. Use distinct colors for each company. Include legend with company names and percentages" -o figures/market_share.png --doc-type report
+
+\begin{figure}[htbp]
+\centering
+% \includegraphics[width=0.8\textwidth]{../figures/market_share.png}
+\caption{Market Share by Company (2024)}
+\label{fig:market_share}
+\end{figure}
+
+\begin{table}[htbp]
+\centering
+\caption{Top 10 Companies by Market Share}
+\begin{tabular}{@{}clrrr@{}}
+\toprule
+\textbf{Rank} & \textbf{Company} & \textbf{Revenue} & \textbf{Share} & \textbf{YoY Growth} \\
+\midrule
+1 & Company A & \$X.XX B & XX.X\% & \trendup{} XX\% \\
+\rowcolor{tablealt} 2 & Company B & \$X.XX B & XX.X\% & \trendup{} XX\% \\
+3 & Company C & \$X.XX B & XX.X\% & \trendflat{} XX\% \\
+\rowcolor{tablealt} 4 & Company D & \$X.XX B & XX.X\% & \trendup{} XX\% \\
+5 & Company E & \$X.XX B & XX.X\% & \trenddown{} XX\% \\
+\rowcolor{tablealt} 6 & Company F & \$X.XX B & XX.X\% & \trendup{} XX\% \\
+7 & Company G & \$X.XX B & XX.X\% & \trendup{} XX\% \\
+\rowcolor{tablealt} 8 & Company H & \$X.XX B & XX.X\% & \trendflat{} XX\% \\
+9 & Company I & \$X.XX B & XX.X\% & \trendup{} XX\% \\
+\rowcolor{tablealt} 10 & Company J & \$X.XX B & XX.X\% & \trenddown{} XX\% \\
+\midrule
+& Others & \$X.XX B & XX.X\% & -- \\
+\bottomrule
+\end{tabular}
+\label{tab:market_share}
+\end{table}
+
+\section{Competitive Positioning}
+
+% VISUAL: Competitive positioning matrix
+% python skills/scientific-schematics/scripts/generate_schematic.py "2x2 competitive positioning matrix. X-axis: 'Market Focus' from Niche (left) to Broad (right). Y-axis: 'Solution Approach' from Product (bottom) to Platform (top). Plot 8-10 companies as labeled circles of varying sizes (representing market share). Include quadrant labels" -o figures/competitive_positioning.png --doc-type report
+
+\begin{figure}[htbp]
+\centering
+% \includegraphics[width=0.9\textwidth]{../figures/competitive_positioning.png}
+\caption{Competitive Positioning Matrix}
+\label{fig:competitive_positioning}
+\end{figure}
+
+[Analyze how competitors are positioned in the market based on key dimensions:]
+
+\subsection{Strategic Groups}
+
+% VISUAL: Strategic group map
+% python skills/scientific-schematics/scripts/generate_schematic.py "Strategic group map with circles representing different strategic groups. X-axis: Geographic Scope (Regional to Global). Y-axis: Product Breadth (Narrow to Broad). Each circle contains multiple company names and is sized by collective market share. 4-5 distinct groups" -o figures/strategic_groups.png --doc-type report
+
+\begin{figure}[htbp]
+\centering
+% \includegraphics[width=0.85\textwidth]{../figures/strategic_groups.png}
+\caption{Strategic Group Mapping}
+\label{fig:strategic_groups}
+\end{figure}
+
+[Identify and describe strategic groups within the competitive landscape]
+
+\section{Competitive Dynamics}
+
+[Analyze competitive behaviors and dynamics:
+- Recent M\&A activity
+- Partnership announcements
+- Product launches
+- Pricing trends
+- Geographic expansion]
+
+\section{Barriers to Entry}
+
+[Analyze barriers that protect incumbents and challenge new entrants:
+- Capital requirements
+- Regulatory barriers
+- Technology barriers
+- Brand and reputation
+- Distribution access
+- Economies of scale]
+
+% ============================================================================
+% CHAPTER 5: CUSTOMER ANALYSIS & SEGMENTATION (4-5 pages)
+% ============================================================================
+\chapter{Customer Analysis \& Segmentation}
+
+\section{Customer Segmentation}
+
+% VISUAL: Customer segmentation
+% python skills/scientific-schematics/scripts/generate_schematic.py "Treemap or pie chart showing customer segments. Segment A XX% (large enterprises), Segment B XX% (mid-market), Segment C XX% (SMB), Segment D XX% (other). Size represents market share. Use distinct colors" -o figures/customer_segments.png --doc-type report
+
+\begin{figure}[htbp]
+\centering
+% \includegraphics[width=0.85\textwidth]{../figures/customer_segments.png}
+\caption{Customer Segmentation by Market Share}
+\label{fig:customer_segments}
+\end{figure}
+
+\begin{table}[htbp]
+\centering
+\caption{Customer Segment Analysis}
+\begin{tabular}{@{}lrrrr@{}}
+\toprule
+\textbf{Segment} & \textbf{Size} & \textbf{Growth} & \textbf{Avg. Deal} & \textbf{CAC} \\
+\midrule
+Large Enterprise & \$X.XX B & XX\% & \$XXX K & \$XX K \\
+\rowcolor{tablealt} Mid-Market & \$X.XX B & XX\% & \$XX K & \$X K \\
+SMB & \$X.XX B & XX\% & \$X K & \$X K \\
+\rowcolor{tablealt} Consumer & \$X.XX B & XX\% & \$XXX & \$XX \\
+\bottomrule
+\end{tabular}
+\label{tab:customer_segments}
+\end{table}
+
+\subsection{Segment A: [Large Enterprise]}
+[Detailed segment analysis including:
+- Segment characteristics
+- Buying behavior
+- Key needs and pain points
+- Decision-making process
+- Willingness to pay]
+
+\subsection{Segment B: [Mid-Market]}
+[Detailed segment analysis]
+
+\subsection{Segment C: [SMB]}
+[Detailed segment analysis]
+
+\subsection{Segment D: [Other]}
+[Detailed segment analysis]
+
+\section{Segment Attractiveness}
+
+% VISUAL: Segment attractiveness matrix
+% python skills/scientific-schematics/scripts/generate_schematic.py "2x2 segment attractiveness matrix. X-axis: Segment Size (Small to Large). Y-axis: Growth Rate (Low to High). Plot customer segments as circles. Upper-right: 'Priority', Upper-left: 'Invest to Grow', Lower-right: 'Harvest', Lower-left: 'Deprioritize'. Include segment labels" -o figures/segment_attractiveness.png --doc-type report
+
+\begin{figure}[htbp]
+\centering
+% \includegraphics[width=0.85\textwidth]{../figures/segment_attractiveness.png}
+\caption{Customer Segment Attractiveness Matrix}
+\label{fig:segment_attractiveness}
+\end{figure}
+
+[Analyze which segments are most attractive for investment and focus]
+
+\section{Customer Needs Analysis}
+
+[Identify and prioritize customer needs by segment:
+- Functional needs
+- Emotional needs
+- Social needs
+- Pain points
+- Unmet needs]
+
+\section{Buying Behavior}
+
+[Analyze how customers buy in this market:
+- Purchase triggers
+- Decision-making process
+- Key influencers
+- Evaluation criteria
+- Purchase channels]
+
+% VISUAL: Customer journey
+% python skills/scientific-schematics/scripts/generate_schematic.py "Customer journey diagram showing 5 stages: Awareness → Consideration → Decision → Implementation → Advocacy. Each stage shows key activities, pain points, and touchpoints. Use horizontal flow with icons for each stage" -o figures/customer_journey.png --doc-type report
+
+\begin{figure}[htbp]
+\centering
+% \includegraphics[width=\textwidth]{../figures/customer_journey.png}
+\caption{Customer Journey Map}
+\label{fig:customer_journey}
+\end{figure}
+
+% ============================================================================
+% CHAPTER 6: TECHNOLOGY & INNOVATION LANDSCAPE (4-5 pages)
+% ============================================================================
+\chapter{Technology \& Innovation Landscape}
+
+\section{Current Technology Stack}
+
+[Describe the technology infrastructure and stack commonly used in the market]
+
+\section{Technology Roadmap}
+
+% VISUAL: Technology roadmap
+% python skills/scientific-schematics/scripts/generate_schematic.py "Technology roadmap timeline from 2024 to 2030. Show 3 parallel tracks: Core Technology (blue), Emerging Technology (green), and Enabling Technology (orange). Mark key milestones and technology introductions on each track. Use horizontal timeline format" -o figures/technology_roadmap.png --doc-type report
+
+\begin{figure}[htbp]
+\centering
+% \includegraphics[width=\textwidth]{../figures/technology_roadmap.png}
+\caption{Technology Evolution Roadmap (2024-2030)}
+\label{fig:tech_roadmap}
+\end{figure}
+
+[Describe how technology is expected to evolve:
+- Near-term (1-2 years)
+- Medium-term (3-5 years)
+- Long-term (5-10 years)]
+
+\section{Emerging Technologies}
+
+[Analyze emerging technologies that could impact the market:
+- Technology description
+- Current maturity level
+- Expected timeline to mainstream adoption
+- Potential impact on market]
+
+\subsection{Technology 1: [Name]}
+[Detailed analysis]
+
+\subsection{Technology 2: [Name]}
+[Detailed analysis]
+
+\subsection{Technology 3: [Name]}
+[Detailed analysis]
+
+\section{Innovation Trends}
+
+% VISUAL: Innovation matrix
+% python skills/scientific-schematics/scripts/generate_schematic.py "Innovation adoption curve or hype cycle diagram showing where key technologies sit. From left to right: Innovation Trigger, Peak of Inflated Expectations, Trough of Disillusionment, Slope of Enlightenment, Plateau of Productivity. Plot 6-8 technologies at different points" -o figures/innovation_curve.png --doc-type report
+
+\begin{figure}[htbp]
+\centering
+% \includegraphics[width=\textwidth]{../figures/innovation_curve.png}
+\caption{Technology Adoption Curve / Hype Cycle}
+\label{fig:innovation}
+\end{figure}
+
+[Analyze innovation trends and R\&D activity:
+- R\&D investment levels
+- Patent filing trends
+- Startup activity
+- Corporate innovation initiatives]
+
+\section{Technology Adoption Barriers}
+
+[Identify barriers to technology adoption:
+- Technical complexity
+- Integration challenges
+- Cost barriers
+- Skills gaps
+- Security/privacy concerns]
+
+% ============================================================================
+% CHAPTER 7: REGULATORY & POLICY ENVIRONMENT (3-4 pages)
+% ============================================================================
+\chapter{Regulatory \& Policy Environment}
+
+\section{Current Regulatory Framework}
+
+[Describe the current regulatory landscape:
+- Key regulations
+- Regulatory bodies
+- Compliance requirements
+- Enforcement mechanisms]
+
+\section{Regulatory Timeline}
+
+% VISUAL: Regulatory timeline
+% python skills/scientific-schematics/scripts/generate_schematic.py "Regulatory timeline from 2020 to 2028. Show key regulatory milestones as markers on horizontal timeline. Past events in dark blue, future/upcoming in light blue. Include regulation names and effective dates. Mark current date with vertical line" -o figures/regulatory_timeline.png --doc-type report
+
+\begin{figure}[htbp]
+\centering
+% \includegraphics[width=\textwidth]{../figures/regulatory_timeline.png}
+\caption{Regulatory Development Timeline}
+\label{fig:regulatory_timeline}
+\end{figure}
+
+[Chronological analysis of regulatory developments]
+
+\section{Regulatory Impact Analysis}
+
+[Analyze how regulations impact the market:
+- Compliance costs
+- Market access implications
+- Competitive implications
+- Product/service requirements]
+
+\section{Policy Trends}
+
+[Identify policy trends that could affect the market:
+- Government priorities
+- Funding initiatives
+- Trade policies
+- Environmental policies]
+
+\section{Regional Regulatory Differences}
+
+[Compare regulatory environments across regions:
+- North America
+- Europe
+- Asia-Pacific
+- Other regions]
+
+% ============================================================================
+% CHAPTER 8: RISK ANALYSIS (3-4 pages)
+% ============================================================================
+\chapter{Risk Analysis}
+
+\section{Risk Overview}
+
+[Provide overview of key risks facing market participants]
+
+\section{Risk Assessment}
+
+% VISUAL: Risk heatmap
+% python skills/scientific-schematics/scripts/generate_schematic.py "Risk heatmap matrix. X-axis: Impact (Low to Critical). Y-axis: Probability (Unlikely to Very Likely). Plot 10-12 risks as labeled circles. Color code: Green (low risk), Yellow (medium), Orange (high), Red (critical). Include risk labels" -o figures/risk_heatmap.png --doc-type report
+
+\begin{figure}[htbp]
+\centering
+% \includegraphics[width=0.9\textwidth]{../figures/risk_heatmap.png}
+\caption{Risk Assessment Heatmap}
+\label{fig:risk_heatmap}
+\end{figure}
+
+\begin{table}[htbp]
+\centering
+\caption{Risk Register Summary}
+\begin{tabular}{@{}llccl@{}}
+\toprule
+\textbf{Risk} & \textbf{Category} & \textbf{Probability} & \textbf{Impact} & \textbf{Rating} \\
+\midrule
+Risk 1 & Market & High & High & \riskhigh{} \\
+\rowcolor{tablealt} Risk 2 & Regulatory & Medium & High & \riskhigh{} \\
+Risk 3 & Technology & Medium & Medium & \riskmedium{} \\
+\rowcolor{tablealt} Risk 4 & Competitive & High & Medium & \riskmedium{} \\
+Risk 5 & Operational & Low & High & \riskmedium{} \\
+\rowcolor{tablealt} Risk 6 & Financial & Low & Medium & \risklow{} \\
+\bottomrule
+\end{tabular}
+\label{tab:risk_register}
+\end{table}
+
+\subsection{Market Risks}
+[Detailed analysis of market-related risks]
+
+\subsection{Competitive Risks}
+[Detailed analysis of competitive risks]
+
+\subsection{Regulatory Risks}
+[Detailed analysis of regulatory risks]
+
+\subsection{Technology Risks}
+[Detailed analysis of technology risks]
+
+\subsection{Operational Risks}
+[Detailed analysis of operational risks]
+
+\subsection{Financial Risks}
+[Detailed analysis of financial risks]
+
+\section{Risk Mitigation Strategies}
+
+% VISUAL: Risk mitigation matrix
+% python skills/scientific-schematics/scripts/generate_schematic.py "Risk mitigation matrix showing risks in left column and corresponding mitigation strategies in right column. Connect risks to mitigations with arrows. Color code by risk severity. Include both prevention and response strategies" -o figures/risk_mitigation.png --doc-type report
+
+\begin{figure}[htbp]
+\centering
+% \includegraphics[width=0.9\textwidth]{../figures/risk_mitigation.png}
+\caption{Risk Mitigation Framework}
+\label{fig:risk_mitigation}
+\end{figure}
+
+[Describe strategies to mitigate identified risks]
+
+\begin{riskbox}[Risk Mitigation Summary]
+\begin{enumerate}
+ \item \textbf{[Risk 1]:} [Mitigation strategy]
+ \item \textbf{[Risk 2]:} [Mitigation strategy]
+ \item \textbf{[Risk 3]:} [Mitigation strategy]
+ \item \textbf{[Risk 4]:} [Mitigation strategy]
+\end{enumerate}
+\end{riskbox}
+
+% ============================================================================
+% CHAPTER 9: STRATEGIC OPPORTUNITIES & RECOMMENDATIONS (4-5 pages)
+% ============================================================================
+\chapter{Strategic Opportunities \& Recommendations}
+
+\section{Opportunity Analysis}
+
+% VISUAL: Opportunity matrix
+% python skills/scientific-schematics/scripts/generate_schematic.py "2x2 opportunity matrix. X-axis: Market Attractiveness (Low to High). Y-axis: Ability to Win (Low to High). Plot 6-8 opportunities as labeled circles of varying sizes. Upper-right: 'Pursue Aggressively', Upper-left: 'Selective Investment', Lower-right: 'Build Capabilities', Lower-left: 'Avoid'" -o figures/opportunity_matrix.png --doc-type report
+
+\begin{figure}[htbp]
+\centering
+% \includegraphics[width=0.9\textwidth]{../figures/opportunity_matrix.png}
+\caption{Strategic Opportunity Assessment Matrix}
+\label{fig:opportunity_matrix}
+\end{figure}
+
+[Identify and analyze strategic opportunities in the market]
+
+\subsection{Opportunity 1: [Name]}
+\begin{opportunitybox}[Opportunity: [Name]]
+\textbf{Description:} [Brief description]
+
+\textbf{Market Size:} \marketsize{X.X billion}
+
+\textbf{Growth Rate:} \growthrate{XX.X}
+
+\textbf{Strategic Fit:} \rating{4}
+
+\textbf{Investment Required:} \$XX million
+\end{opportunitybox}
+
+[Detailed analysis of the opportunity]
+
+\subsection{Opportunity 2: [Name]}
+[Detailed analysis]
+
+\subsection{Opportunity 3: [Name]}
+[Detailed analysis]
+
+\section{Strategic Options Analysis}
+
+[Analyze different strategic approaches:
+- Build (organic development)
+- Buy (M\&A)
+- Partner (strategic alliances)
+- Ignore (not pursue)]
+
+\section{Prioritized Recommendations}
+
+% VISUAL: Recommendation priority matrix
+% python skills/scientific-schematics/scripts/generate_schematic.py "Priority matrix showing recommendations. X-axis: Effort/Investment (Low to High). Y-axis: Impact/Value (Low to High). Plot 6-8 recommendations. Upper-left: 'Quick Wins', Upper-right: 'Major Projects', Lower-left: 'Fill-ins', Lower-right: 'Thankless Tasks'. Label each recommendation" -o figures/recommendation_priority.png --doc-type report
+
+\begin{figure}[htbp]
+\centering
+% \includegraphics[width=0.85\textwidth]{../figures/recommendation_priority.png}
+\caption{Recommendation Priority Framework}
+\label{fig:recommendations}
+\end{figure}
+
+\begin{recommendationbox}[Strategic Recommendations]
+\textbf{Tier 1: Immediate Priority}
+\begin{enumerate}
+ \item \textbf{[Recommendation 1]:} [Detailed action with expected outcome, timeline, and investment]
+ \item \textbf{[Recommendation 2]:} [Detailed action]
+\end{enumerate}
+
+\textbf{Tier 2: Near-Term (6-12 months)}
+\begin{enumerate}[start=3]
+ \item \textbf{[Recommendation 3]:} [Detailed action]
+ \item \textbf{[Recommendation 4]:} [Detailed action]
+\end{enumerate}
+
+\textbf{Tier 3: Medium-Term (1-2 years)}
+\begin{enumerate}[start=5]
+ \item \textbf{[Recommendation 5]:} [Detailed action]
+ \item \textbf{[Recommendation 6]:} [Detailed action]
+\end{enumerate}
+\end{recommendationbox}
+
+\section{Success Factors}
+
+[Identify critical success factors for implementing recommendations:
+- Organizational capabilities
+- Resource requirements
+- Timing considerations
+- External dependencies]
+
+% ============================================================================
+% CHAPTER 10: IMPLEMENTATION ROADMAP (3-4 pages)
+% ============================================================================
+\chapter{Implementation Roadmap}
+
+\section{Implementation Overview}
+
+[Provide overview of implementation approach and timeline]
+
+\section{Phased Implementation Plan}
+
+% VISUAL: Implementation timeline
+% python skills/scientific-schematics/scripts/generate_schematic.py "Gantt chart style implementation timeline showing 4 phases over 24 months. Phase 1: Foundation (months 1-6), Phase 2: Build (months 4-12), Phase 3: Scale (months 10-18), Phase 4: Optimize (months 16-24). Show overlapping phases with key milestones marked. Use different colors for each phase" -o figures/implementation_timeline.png --doc-type report
+
+\begin{figure}[htbp]
+\centering
+% \includegraphics[width=\textwidth]{../figures/implementation_timeline.png}
+\caption{Implementation Roadmap Timeline}
+\label{fig:implementation}
+\end{figure}
+
+\subsection{Phase 1: Foundation (Months 1-6)}
+[Detailed activities and deliverables for Phase 1]
+
+\subsection{Phase 2: Build (Months 4-12)}
+[Detailed activities and deliverables for Phase 2]
+
+\subsection{Phase 3: Scale (Months 10-18)}
+[Detailed activities and deliverables for Phase 3]
+
+\subsection{Phase 4: Optimize (Months 16-24)}
+[Detailed activities and deliverables for Phase 4]
+
+\section{Key Milestones}
+
+% VISUAL: Milestone tracker
+% python skills/scientific-schematics/scripts/generate_schematic.py "Milestone tracker showing 8-10 key milestones on a horizontal timeline. Each milestone has a date, name, and status indicator (completed=green checkmark, in-progress=yellow circle, upcoming=gray circle). Group by phase" -o figures/milestone_tracker.png --doc-type report
+
+\begin{figure}[htbp]
+\centering
+% \includegraphics[width=\textwidth]{../figures/milestone_tracker.png}
+\caption{Key Implementation Milestones}
+\label{fig:milestones}
+\end{figure}
+
+\begin{table}[htbp]
+\centering
+\caption{Implementation Milestones}
+\begin{tabular}{@{}llll@{}}
+\toprule
+\textbf{Milestone} & \textbf{Target Date} & \textbf{Owner} & \textbf{Success Criteria} \\
+\midrule
+Milestone 1 & Month 3 & [Owner] & [Criteria] \\
+\rowcolor{tablealt} Milestone 2 & Month 6 & [Owner] & [Criteria] \\
+Milestone 3 & Month 9 & [Owner] & [Criteria] \\
+\rowcolor{tablealt} Milestone 4 & Month 12 & [Owner] & [Criteria] \\
+Milestone 5 & Month 18 & [Owner] & [Criteria] \\
+\rowcolor{tablealt} Milestone 6 & Month 24 & [Owner] & [Criteria] \\
+\bottomrule
+\end{tabular}
+\label{tab:milestones}
+\end{table}
+
+\section{Resource Requirements}
+
+[Detail resource requirements for implementation:
+- Team structure
+- Budget allocation
+- Technology requirements
+- External support needs]
+
+\section{Governance Structure}
+
+[Define governance for implementation:
+- Decision-making authority
+- Reporting structure
+- Review cadence
+- Escalation paths]
+
+% ============================================================================
+% CHAPTER 11: INVESTMENT THESIS & FINANCIAL PROJECTIONS (3-4 pages)
+% ============================================================================
+\chapter{Investment Thesis \& Financial Projections}
+
+\section{Investment Summary}
+
+[Summarize the investment opportunity:
+- Key value drivers
+- Expected returns
+- Investment timeline
+- Risk-adjusted assessment]
+
+\begin{executivesummarybox}[Investment Thesis]
+The \reporttitle{} market presents a compelling investment opportunity characterized by:
+
+\begin{itemize}
+ \item \textbf{Large Market:} \marketsize{XX billion} TAM growing at \growthrate{XX.X} CAGR
+ \item \textbf{Favorable Dynamics:} [Key market dynamics]
+ \item \textbf{Strong Drivers:} [Key growth drivers]
+ \item \textbf{Manageable Risks:} [Risk summary]
+ \item \textbf{Clear Path to Value:} [Value creation summary]
+\end{itemize}
+\end{executivesummarybox}
+
+\section{Financial Projections}
+
+% VISUAL: Financial projections
+% python skills/scientific-schematics/scripts/generate_schematic.py "Financial projections chart showing revenue growth over 5 years. Bar chart for revenue with line overlay for growth rate. Three scenarios: Conservative (gray bars), Base Case (blue bars), Optimistic (green bars). Y-axis dual: Revenue ($M) and Growth (%). Include data labels" -o figures/financial_projections.png --doc-type report
+
+\begin{figure}[htbp]
+\centering
+% \includegraphics[width=0.9\textwidth]{../figures/financial_projections.png}
+\caption{Financial Projections (5-Year)}
+\label{fig:financials}
+\end{figure}
+
+\begin{table}[htbp]
+\centering
+\caption{Financial Projections Summary}
+\begin{tabular}{@{}lrrrrr@{}}
+\toprule
+\textbf{Metric} & \textbf{Year 1} & \textbf{Year 2} & \textbf{Year 3} & \textbf{Year 4} & \textbf{Year 5} \\
+\midrule
+Revenue (\$M) & \$XX & \$XX & \$XX & \$XX & \$XX \\
+\rowcolor{tablealt} Growth Rate & XX\% & XX\% & XX\% & XX\% & XX\% \\
+Gross Margin & XX\% & XX\% & XX\% & XX\% & XX\% \\
+\rowcolor{tablealt} EBITDA (\$M) & \$XX & \$XX & \$XX & \$XX & \$XX \\
+EBITDA Margin & XX\% & XX\% & XX\% & XX\% & XX\% \\
+\bottomrule
+\end{tabular}
+\label{tab:financials}
+\end{table}
+
+\section{Scenario Analysis}
+
+% VISUAL: Scenario comparison
+% python skills/scientific-schematics/scripts/generate_schematic.py "Scenario comparison chart showing 3 scenarios (Conservative, Base, Optimistic) across key metrics. Use grouped bar chart with metrics on X-axis (Revenue Y5, EBITDA Y5, Market Share, ROI) and values on Y-axis. Color code by scenario" -o figures/scenario_analysis.png --doc-type report
+
+\begin{figure}[htbp]
+\centering
+% \includegraphics[width=0.85\textwidth]{../figures/scenario_analysis.png}
+\caption{Scenario Analysis Comparison}
+\label{fig:scenarios}
+\end{figure}
+
+\subsection{Conservative Scenario}
+[Detailed assumptions and outcomes for conservative case]
+
+\subsection{Base Case Scenario}
+[Detailed assumptions and outcomes for base case]
+
+\subsection{Optimistic Scenario}
+[Detailed assumptions and outcomes for optimistic case]
+
+\section{Key Assumptions}
+
+[Document key assumptions underlying financial projections:
+- Market growth assumptions
+- Pricing assumptions
+- Cost assumptions
+- Competitive assumptions
+- Timing assumptions]
+
+\section{Sensitivity Analysis}
+
+[Analyze sensitivity of projections to key variables:
+- Revenue sensitivity to market growth
+- Margin sensitivity to pricing
+- Returns sensitivity to timing]
+
+\section{Return Expectations}
+
+[Summarize expected returns:
+- ROI projections
+- Payback period
+- IRR estimates
+- Multiple analysis]
+
+% ============================================================================
+% APPENDICES
+% ============================================================================
+\appendix
+
+% ============================================================================
+% APPENDIX A: METHODOLOGY & DATA SOURCES
+% ============================================================================
+\chapter{Methodology \& Data Sources}
+
+\section{Research Methodology}
+
+[Describe the research methodology used:
+- Primary research methods
+- Secondary research sources
+- Data collection timeframe
+- Analytical frameworks applied]
+
+\section{Data Sources}
+
+[List all data sources used in the report:
+- Market research reports
+- Industry databases
+- Government statistics
+- Company reports
+- Expert interviews
+- Academic publications]
+
+\section{Limitations}
+
+[Acknowledge limitations of the analysis:
+- Data availability constraints
+- Methodological limitations
+- Forecast uncertainty
+- Scope limitations]
+
+% ============================================================================
+% APPENDIX B: DETAILED MARKET DATA
+% ============================================================================
+\chapter{Detailed Market Data}
+
+\section{Historical Market Data}
+
+[Provide detailed historical market data tables]
+
+\section{Regional Data Breakdown}
+
+[Provide detailed regional market data]
+
+\section{Segment Data Details}
+
+[Provide detailed segment-level data]
+
+\section{Competitive Data}
+
+[Provide detailed competitive data tables]
+
+% ============================================================================
+% APPENDIX C: COMPANY PROFILES
+% ============================================================================
+\chapter{Company Profiles}
+
+\section{Company A}
+
+\begin{calloutbox}[Company Profile: Company A]
+\textbf{Headquarters:} [Location]
+
+\textbf{Revenue:} \$X.X billion (FY2024)
+
+\textbf{Employees:} X,XXX
+
+\textbf{Market Position:} [Position description]
+
+\textbf{Key Products/Services:} [List]
+
+\textbf{Recent Developments:} [Summary]
+\end{calloutbox}
+
+[Brief narrative description of company strategy and positioning]
+
+\section{Company B}
+[Company profile]
+
+\section{Company C}
+[Company profile]
+
+\section{Company D}
+[Company profile]
+
+\section{Company E}
+[Company profile]
+
+% ============================================================================
+% REFERENCES
+% ============================================================================
+\newpage
+\bibliographystyle{plainnat}
+\bibliography{../references/references}
+
+% Alternative: Manual bibliography if not using BibTeX
+% \begin{thebibliography}{99}
+%
+% \bibitem{source1}
+% Author1, A.B. (2024).
+% Title of report or article.
+% \textit{Publisher/Source}.
+% URL
+%
+% \bibitem{source2}
+% [Continue with all references...]
+%
+% \end{thebibliography}
+
+% ============================================================================
+% END OF DOCUMENT
+% ============================================================================
+\end{document}
diff --git a/scientific-skills/market-research-reports/assets/market_research.sty b/scientific-skills/market-research-reports/assets/market_research.sty
new file mode 100644
index 0000000..d383941
--- /dev/null
+++ b/scientific-skills/market-research-reports/assets/market_research.sty
@@ -0,0 +1,564 @@
+% market_research.sty - Professional Market Research Report Styling
+% For use with XeLaTeX or LuaLaTeX
+% Style inspired by top consulting firms (McKinsey, BCG, Gartner)
+
+\ProvidesPackage{market_research}[2024/01/01 Market Research Report Style]
+
+% ============================================================================
+% REQUIRED PACKAGES
+% ============================================================================
+
+% Page layout and geometry
+\RequirePackage[margin=1in]{geometry}
+\RequirePackage{setspace}
+
+% Typography
+\RequirePackage[utf8]{inputenc}
+\RequirePackage[T1]{fontenc}
+\RequirePackage{helvet}
+\renewcommand{\familydefault}{\sfdefault}
+
+% Colors and graphics
+\RequirePackage{xcolor}
+\RequirePackage{graphicx}
+\RequirePackage{tikz}
+
+% Tables
+\RequirePackage{longtable}
+\RequirePackage{booktabs}
+\RequirePackage{multirow}
+\RequirePackage{array}
+\RequirePackage{colortbl}
+
+% Lists and formatting
+\RequirePackage{enumitem}
+\RequirePackage{parskip}
+
+% Boxes and callouts
+\RequirePackage[most]{tcolorbox}
+
+% Headers and footers
+\RequirePackage{fancyhdr}
+\RequirePackage{titlesec}
+
+% Hyperlinks and references
+\RequirePackage{hyperref}
+\RequirePackage[numbers,sort&compress]{natbib}
+
+% Math (for financial projections)
+\RequirePackage{amsmath}
+
+% Captions
+\RequirePackage{caption}
+\RequirePackage{subcaption}
+
+% ============================================================================
+% COLOR DEFINITIONS
+% ============================================================================
+
+% Primary colors (professional blue palette)
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+
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+
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+
+% Recommendation and action colors
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+
+% Neutral colors
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+
+% Chart colors (colorblind-friendly palette)
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+\definecolor{chart6}{RGB}{213, 94, 0} % Vermillion
+\definecolor{chart7}{RGB}{240, 228, 66} % Yellow
+
+% ============================================================================
+% HYPERLINK CONFIGURATION
+% ============================================================================
+
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+ pdfsubject={Market Analysis},
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+% ============================================================================
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+{\chaptertitlename\ \thechapter}{20pt}{\Huge}
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+
+% ============================================================================
+% BOX ENVIRONMENTS
+% ============================================================================
+
+% Key Insight Box (Blue) - For major findings and insights
+\newtcolorbox{keyinsightbox}[1][Key Insight]{
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diff --git a/scientific-skills/market-research-reports/references/data_analysis_patterns.md b/scientific-skills/market-research-reports/references/data_analysis_patterns.md
new file mode 100644
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+# Data Analysis Patterns for Market Research
+
+Templates and frameworks for conducting rigorous market analysis.
+
+---
+
+## Market Sizing Frameworks
+
+### TAM/SAM/SOM Analysis
+
+**Total Addressable Market (TAM)** represents the total revenue opportunity if 100% market share was achieved.
+
+#### Top-Down Approach
+```
+TAM = Total Industry Revenue (from market research reports)
+
+Example:
+- Global AI Software Market (2024): $184 billion
+- Source: Gartner, IDC, or similar
+```
+
+#### Bottom-Up Approach
+```
+TAM = Number of Potential Customers × Average Revenue per Customer
+
+Example:
+- Number of enterprises globally: 400 million
+- Target segment (large enterprises): 50,000
+- Average annual spend on solution: $500,000
+- TAM = 50,000 × $500,000 = $25 billion
+```
+
+**Serviceable Addressable Market (SAM)** represents the portion of TAM that can be served given product/service capabilities.
+
+```
+SAM = TAM × Applicable Segment %
+
+Example:
+- TAM: $25 billion
+- Geographic constraint (North America only): 40%
+- Product fit (enterprise only): 60%
+- SAM = $25B × 40% × 60% = $6 billion
+```
+
+**Serviceable Obtainable Market (SOM)** represents realistic market share capture.
+
+```
+SOM = SAM × Achievable Market Share %
+
+Example:
+- SAM: $6 billion
+- Conservative market share (5%): $300 million
+- Base case market share (10%): $600 million
+- Optimistic market share (15%): $900 million
+```
+
+### Growth Rate Calculation
+
+#### CAGR (Compound Annual Growth Rate)
+```
+CAGR = (End Value / Start Value)^(1/n) - 1
+
+Where n = number of years
+
+Example:
+- 2020 market size: $10 billion
+- 2024 market size: $18 billion
+- n = 4 years
+- CAGR = (18/10)^(1/4) - 1 = 15.8%
+```
+
+#### Year-over-Year Growth
+```
+YoY Growth = (Current Year - Previous Year) / Previous Year × 100
+
+Example:
+- 2023: $15 billion
+- 2024: $18 billion
+- YoY Growth = (18-15)/15 × 100 = 20%
+```
+
+---
+
+## Porter's Five Forces Analysis
+
+### Framework Template
+
+For each force, assess: **HIGH**, **MEDIUM**, or **LOW**
+
+#### 1. Threat of New Entrants
+
+**Factors to evaluate:**
+| Factor | Assessment | Notes |
+|--------|------------|-------|
+| Capital requirements | High/Med/Low | $ required to enter |
+| Economies of scale | Strong/Moderate/Weak | Incumbent advantages |
+| Brand loyalty | High/Med/Low | Customer switching cost |
+| Access to distribution | Easy/Moderate/Difficult | Channel availability |
+| Regulatory barriers | High/Med/Low | Licensing, certifications |
+| Proprietary technology | Critical/Important/Minor | IP and know-how |
+| Expected retaliation | Aggressive/Moderate/Passive | Incumbent response |
+
+**Overall Assessment:** [HIGH/MEDIUM/LOW]
+
+**Key Insights:** [Summary of implications]
+
+#### 2. Bargaining Power of Suppliers
+
+**Factors to evaluate:**
+| Factor | Assessment | Notes |
+|--------|------------|-------|
+| Supplier concentration | High/Med/Low | Number of suppliers |
+| Switching costs | High/Med/Low | Cost to change suppliers |
+| Supplier differentiation | High/Med/Low | Uniqueness of inputs |
+| Forward integration threat | High/Med/Low | Can suppliers compete? |
+| Importance to supplier | Critical/Important/Minor | Your share of their revenue |
+| Substitute inputs | Many/Some/Few | Alternatives available |
+
+**Overall Assessment:** [HIGH/MEDIUM/LOW]
+
+#### 3. Bargaining Power of Buyers
+
+**Factors to evaluate:**
+| Factor | Assessment | Notes |
+|--------|------------|-------|
+| Buyer concentration | High/Med/Low | Few large vs. many small |
+| Purchase volume | Large/Medium/Small | Relative importance |
+| Switching costs | Low/Med/High | Cost to change vendors |
+| Price sensitivity | High/Med/Low | Focus on price vs. value |
+| Backward integration threat | High/Med/Low | Can buyers self-supply? |
+| Information availability | Full/Partial/Limited | Market transparency |
+
+**Overall Assessment:** [HIGH/MEDIUM/LOW]
+
+#### 4. Threat of Substitutes
+
+**Factors to evaluate:**
+| Factor | Assessment | Notes |
+|--------|------------|-------|
+| Substitute availability | Many/Some/Few | Number of alternatives |
+| Price-performance ratio | Better/Same/Worse | Value comparison |
+| Switching costs | Low/Med/High | Friction to substitute |
+| Buyer propensity to switch | High/Med/Low | Willingness to change |
+| Perceived differentiation | Low/Med/High | Unique value |
+
+**Overall Assessment:** [HIGH/MEDIUM/LOW]
+
+#### 5. Competitive Rivalry
+
+**Factors to evaluate:**
+| Factor | Assessment | Notes |
+|--------|------------|-------|
+| Number of competitors | Many/Several/Few | Market fragmentation |
+| Industry growth | Slow/Moderate/Fast | Growth rate impact |
+| Fixed costs | High/Med/Low | Pressure to fill capacity |
+| Product differentiation | Low/Med/High | Commoditization level |
+| Exit barriers | High/Med/Low | Difficulty leaving market |
+| Strategic stakes | High/Med/Low | Importance to competitors |
+
+**Overall Assessment:** [HIGH/MEDIUM/LOW]
+
+### Five Forces Summary Table
+
+| Force | Rating | Key Drivers | Implications |
+|-------|--------|-------------|--------------|
+| New Entrants | [H/M/L] | [Top factors] | [Strategic impact] |
+| Supplier Power | [H/M/L] | [Top factors] | [Strategic impact] |
+| Buyer Power | [H/M/L] | [Top factors] | [Strategic impact] |
+| Substitutes | [H/M/L] | [Top factors] | [Strategic impact] |
+| Rivalry | [H/M/L] | [Top factors] | [Strategic impact] |
+
+**Overall Industry Attractiveness:** [ATTRACTIVE / MODERATE / UNATTRACTIVE]
+
+---
+
+## PESTLE Analysis
+
+### Framework Template
+
+#### Political Factors
+
+| Factor | Current State | Trend | Impact | Time Horizon |
+|--------|---------------|-------|--------|--------------|
+| Government stability | | ↑ ↓ → | H/M/L | Short/Med/Long |
+| Trade policies | | ↑ ↓ → | H/M/L | |
+| Tax regulations | | ↑ ↓ → | H/M/L | |
+| Government support | | ↑ ↓ → | H/M/L | |
+| Political relations | | ↑ ↓ → | H/M/L | |
+
+**Key Political Implications:** [Summary]
+
+#### Economic Factors
+
+| Factor | Current State | Trend | Impact | Time Horizon |
+|--------|---------------|-------|--------|--------------|
+| GDP growth | X.X% | ↑ ↓ → | H/M/L | |
+| Interest rates | X.X% | ↑ ↓ → | H/M/L | |
+| Inflation | X.X% | ↑ ↓ → | H/M/L | |
+| Exchange rates | | ↑ ↓ → | H/M/L | |
+| Consumer spending | | ↑ ↓ → | H/M/L | |
+| Unemployment | X.X% | ↑ ↓ → | H/M/L | |
+
+**Key Economic Implications:** [Summary]
+
+#### Social Factors
+
+| Factor | Current State | Trend | Impact | Time Horizon |
+|--------|---------------|-------|--------|--------------|
+| Demographics | | ↑ ↓ → | H/M/L | |
+| Cultural attitudes | | ↑ ↓ → | H/M/L | |
+| Consumer behavior | | ↑ ↓ → | H/M/L | |
+| Education levels | | ↑ ↓ → | H/M/L | |
+| Health consciousness | | ↑ ↓ → | H/M/L | |
+| Work-life balance | | ↑ ↓ → | H/M/L | |
+
+**Key Social Implications:** [Summary]
+
+#### Technological Factors
+
+| Factor | Current State | Trend | Impact | Time Horizon |
+|--------|---------------|-------|--------|--------------|
+| R&D activity | | ↑ ↓ → | H/M/L | |
+| Technology adoption | | ↑ ↓ → | H/M/L | |
+| Automation | | ↑ ↓ → | H/M/L | |
+| Digital infrastructure | | ↑ ↓ → | H/M/L | |
+| Innovation rate | | ↑ ↓ → | H/M/L | |
+| Disruptive tech | | ↑ ↓ → | H/M/L | |
+
+**Key Technological Implications:** [Summary]
+
+#### Legal Factors
+
+| Factor | Current State | Trend | Impact | Time Horizon |
+|--------|---------------|-------|--------|--------------|
+| Industry regulations | | ↑ ↓ → | H/M/L | |
+| Data protection | | ↑ ↓ → | H/M/L | |
+| Employment law | | ↑ ↓ → | H/M/L | |
+| Consumer protection | | ↑ ↓ → | H/M/L | |
+| IP rights | | ↑ ↓ → | H/M/L | |
+| Antitrust | | ↑ ↓ → | H/M/L | |
+
+**Key Legal Implications:** [Summary]
+
+#### Environmental Factors
+
+| Factor | Current State | Trend | Impact | Time Horizon |
+|--------|---------------|-------|--------|--------------|
+| Climate change | | ↑ ↓ → | H/M/L | |
+| Sustainability reqs | | ↑ ↓ → | H/M/L | |
+| Resource availability | | ↑ ↓ → | H/M/L | |
+| Waste management | | ↑ ↓ → | H/M/L | |
+| Carbon regulations | | ↑ ↓ → | H/M/L | |
+| Environmental awareness | | ↑ ↓ → | H/M/L | |
+
+**Key Environmental Implications:** [Summary]
+
+---
+
+## SWOT Analysis
+
+### Framework Template
+
+#### Strengths (Internal, Positive)
+| Strength | Evidence | Strategic Value |
+|----------|----------|-----------------|
+| [Strength 1] | [Data/proof] | High/Med/Low |
+| [Strength 2] | [Data/proof] | High/Med/Low |
+| [Strength 3] | [Data/proof] | High/Med/Low |
+
+**Core Strengths Summary:** [2-3 sentence synthesis]
+
+#### Weaknesses (Internal, Negative)
+| Weakness | Evidence | Severity |
+|----------|----------|----------|
+| [Weakness 1] | [Data/proof] | Critical/Moderate/Minor |
+| [Weakness 2] | [Data/proof] | Critical/Moderate/Minor |
+| [Weakness 3] | [Data/proof] | Critical/Moderate/Minor |
+
+**Key Vulnerabilities Summary:** [2-3 sentence synthesis]
+
+#### Opportunities (External, Positive)
+| Opportunity | Size/Potential | Timeframe |
+|-------------|----------------|-----------|
+| [Opportunity 1] | $X / High/Med/Low | Short/Med/Long |
+| [Opportunity 2] | $X / High/Med/Low | Short/Med/Long |
+| [Opportunity 3] | $X / High/Med/Low | Short/Med/Long |
+
+**Priority Opportunities Summary:** [2-3 sentence synthesis]
+
+#### Threats (External, Negative)
+| Threat | Likelihood | Impact |
+|--------|------------|--------|
+| [Threat 1] | High/Med/Low | High/Med/Low |
+| [Threat 2] | High/Med/Low | High/Med/Low |
+| [Threat 3] | High/Med/Low | High/Med/Low |
+
+**Critical Threats Summary:** [2-3 sentence synthesis]
+
+### SWOT Strategy Matrix
+
+| | **Strengths** | **Weaknesses** |
+|---|---------------|----------------|
+| **Opportunities** | **SO Strategies** (use strengths to capture opportunities) | **WO Strategies** (overcome weaknesses to capture opportunities) |
+| **Threats** | **ST Strategies** (use strengths to mitigate threats) | **WT Strategies** (minimize weaknesses and avoid threats) |
+
+---
+
+## BCG Growth-Share Matrix
+
+### Framework Template
+
+**Axes:**
+- X-axis: Relative Market Share (High → Low, logarithmic scale)
+- Y-axis: Market Growth Rate (High → Low, typically 10% as midpoint)
+
+### Quadrant Definitions
+
+| Quadrant | Growth | Share | Characteristics | Strategy |
+|----------|--------|-------|-----------------|----------|
+| **Stars** | High | High | Market leaders in growing markets | Invest to maintain position |
+| **Cash Cows** | Low | High | Market leaders in mature markets | Harvest for cash flow |
+| **Question Marks** | High | Low | Small share in growing markets | Invest selectively or divest |
+| **Dogs** | Low | Low | Small share in mature markets | Divest or minimize investment |
+
+### Product/Business Unit Analysis
+
+| Product/BU | Market Growth | Relative Share | Quadrant | Recommended Strategy |
+|------------|---------------|----------------|----------|---------------------|
+| [Product A] | X.X% | X.X | Star/Cow/QM/Dog | [Strategy] |
+| [Product B] | X.X% | X.X | Star/Cow/QM/Dog | [Strategy] |
+| [Product C] | X.X% | X.X | Star/Cow/QM/Dog | [Strategy] |
+
+### Portfolio Balance Assessment
+
+| Quadrant | Number of Products | Revenue % | Investment Priority |
+|----------|-------------------|-----------|---------------------|
+| Stars | X | X% | High |
+| Cash Cows | X | X% | Maintain |
+| Question Marks | X | X% | Selective |
+| Dogs | X | X% | Low/Divest |
+
+---
+
+## Value Chain Analysis
+
+### Framework Template
+
+#### Primary Activities
+
+| Activity | Description | Value Created | Cost | Competitive Position |
+|----------|-------------|---------------|------|---------------------|
+| **Inbound Logistics** | Receiving, storing, inventory | | $X | Strong/Average/Weak |
+| **Operations** | Manufacturing, assembly | | $X | Strong/Average/Weak |
+| **Outbound Logistics** | Distribution, delivery | | $X | Strong/Average/Weak |
+| **Marketing & Sales** | Promotion, sales force | | $X | Strong/Average/Weak |
+| **Service** | Installation, support, repair | | $X | Strong/Average/Weak |
+
+#### Support Activities
+
+| Activity | Description | Value Created | Cost | Competitive Position |
+|----------|-------------|---------------|------|---------------------|
+| **Infrastructure** | Management, finance, legal | | $X | Strong/Average/Weak |
+| **HR Management** | Recruiting, training, comp | | $X | Strong/Average/Weak |
+| **Technology Dev** | R&D, process improvement | | $X | Strong/Average/Weak |
+| **Procurement** | Purchasing, supplier mgmt | | $X | Strong/Average/Weak |
+
+### Value Chain Margin Analysis
+
+```
+Total Revenue: $XXX
+- Inbound Logistics: ($XX)
+- Operations: ($XX)
+- Outbound Logistics: ($XX)
+- Marketing & Sales: ($XX)
+- Service: ($XX)
+- Support Activities: ($XX)
+= Margin: $XX (X%)
+```
+
+### Competitive Comparison
+
+| Activity | Company | Industry Avg | Best-in-Class | Gap |
+|----------|---------|--------------|---------------|-----|
+| [Activity] | X% | Y% | Z% | +/-X% |
+
+---
+
+## Competitive Positioning Analysis
+
+### Framework Template
+
+#### Positioning Dimensions
+
+Common positioning dimension pairs:
+- Price vs. Quality
+- Market Focus (Niche vs. Broad)
+- Solution Type (Product vs. Platform)
+- Geographic Scope (Regional vs. Global)
+- Customer Focus (Enterprise vs. SMB vs. Consumer)
+- Innovation Level (Leader vs. Follower)
+
+#### Competitor Mapping
+
+| Competitor | Dimension 1 Score (1-10) | Dimension 2 Score (1-10) | Market Share | Notes |
+|------------|-------------------------|-------------------------|--------------|-------|
+| Company A | X | X | X% | [Position description] |
+| Company B | X | X | X% | [Position description] |
+| Company C | X | X | X% | [Position description] |
+
+#### Strategic Group Identification
+
+| Strategic Group | Companies | Characteristics | Market Share |
+|-----------------|-----------|-----------------|--------------|
+| Group 1: [Name] | A, B, C | [Description] | X% |
+| Group 2: [Name] | D, E | [Description] | X% |
+| Group 3: [Name] | F, G, H | [Description] | X% |
+
+---
+
+## Risk Assessment Framework
+
+### Risk Identification
+
+#### Risk Categories
+1. **Market Risks**: Demand changes, price pressure, market shifts
+2. **Competitive Risks**: New entrants, competitor moves, disruption
+3. **Regulatory Risks**: New regulations, compliance requirements
+4. **Technology Risks**: Obsolescence, security, integration
+5. **Operational Risks**: Supply chain, quality, capacity
+6. **Financial Risks**: Currency, interest rates, credit
+7. **Reputational Risks**: Brand damage, social media, ethics
+
+### Risk Assessment Matrix
+
+| Risk ID | Risk Description | Category | Probability | Impact | Score | Priority |
+|---------|------------------|----------|-------------|--------|-------|----------|
+| R1 | [Description] | Market | 1-5 | 1-5 | P×I | H/M/L |
+| R2 | [Description] | Competitive | 1-5 | 1-5 | P×I | H/M/L |
+
+**Scoring Guide:**
+- Probability: 1=Very Unlikely, 2=Unlikely, 3=Possible, 4=Likely, 5=Very Likely
+- Impact: 1=Minimal, 2=Minor, 3=Moderate, 4=Major, 5=Severe
+- Priority: Score 15-25=High, 8-14=Medium, 1-7=Low
+
+### Risk Mitigation Planning
+
+| Risk ID | Risk | Mitigation Strategy | Owner | Timeline | Cost |
+|---------|------|---------------------|-------|----------|------|
+| R1 | [Risk] | [Prevention + Response] | [Name] | [Date] | $X |
+
+---
+
+## Financial Analysis Patterns
+
+### Revenue Projection Model
+
+```
+Year N Revenue = Year N-1 Revenue × (1 + Growth Rate)
+
+Or bottom-up:
+Revenue = Customers × Revenue per Customer × Retention Rate
+ + New Customers × Revenue per Customer × (1 - Churn Rate)
+```
+
+### Scenario Analysis Template
+
+| Metric | Conservative | Base Case | Optimistic |
+|--------|--------------|-----------|------------|
+| Market Growth | X% | Y% | Z% |
+| Market Share | X% | Y% | Z% |
+| Pricing | $X | $Y | $Z |
+| Gross Margin | X% | Y% | Z% |
+| **Revenue Y5** | $X | $Y | $Z |
+| **EBITDA Y5** | $X | $Y | $Z |
+
+### Key Financial Metrics
+
+| Metric | Formula | Target |
+|--------|---------|--------|
+| Gross Margin | (Revenue - COGS) / Revenue | X% |
+| EBITDA Margin | EBITDA / Revenue | X% |
+| Customer Acquisition Cost | Sales & Marketing / New Customers | $X |
+| Lifetime Value | ARPU × Gross Margin × Lifetime | $X |
+| LTV/CAC Ratio | LTV / CAC | >3x |
+| Payback Period | CAC / (ARPU × Gross Margin × 12) | Path:
+ """Get the path to the appropriate generation script."""
+ base_path = Path(__file__).parent.parent.parent # skills directory
+
+ if tool == "scientific-schematics":
+ return base_path / "scientific-schematics" / "scripts" / "generate_schematic.py"
+ elif tool == "generate-image":
+ return base_path / "generate-image" / "scripts" / "generate_image.py"
+ else:
+ raise ValueError(f"Unknown tool: {tool}")
+
+
+def generate_visual(
+ filename: str,
+ tool: str,
+ prompt: str,
+ output_dir: Path,
+ topic: str,
+ skip_existing: bool = False,
+ verbose: bool = False
+) -> bool:
+ """Generate a single visual using the appropriate tool."""
+ output_path = output_dir / filename
+
+ # Skip if exists and skip_existing is True
+ if skip_existing and output_path.exists():
+ if verbose:
+ print(f" [SKIP] {filename} already exists")
+ return True
+
+ # Format prompt with topic
+ formatted_prompt = prompt.format(topic=topic)
+
+ # Get script path
+ script_path = get_script_path(tool)
+
+ if not script_path.exists():
+ print(f" [ERROR] Script not found: {script_path}")
+ return False
+
+ # Build command
+ if tool == "scientific-schematics":
+ cmd = [
+ sys.executable,
+ str(script_path),
+ formatted_prompt,
+ "-o", str(output_path),
+ "--doc-type", "report"
+ ]
+ else: # generate-image
+ cmd = [
+ sys.executable,
+ str(script_path),
+ formatted_prompt,
+ "--output", str(output_path)
+ ]
+
+ if verbose:
+ print(f" [GEN] {filename}")
+ print(f" Tool: {tool}")
+ print(f" Prompt: {formatted_prompt[:80]}...")
+
+ try:
+ result = subprocess.run(
+ cmd,
+ capture_output=True,
+ text=True,
+ timeout=120 # 2 minute timeout per image
+ )
+
+ if result.returncode == 0:
+ if verbose:
+ print(f" [OK] {filename} generated successfully")
+ return True
+ else:
+ print(f" [ERROR] {filename} failed:")
+ if result.stderr:
+ print(f" {result.stderr[:200]}")
+ return False
+
+ except subprocess.TimeoutExpired:
+ print(f" [TIMEOUT] {filename} generation timed out")
+ return False
+ except Exception as e:
+ print(f" [ERROR] {filename}: {str(e)}")
+ return False
+
+
+def main():
+ parser = argparse.ArgumentParser(
+ description="Generate visuals for a market research report (default: 5-6 core visuals)"
+ )
+ parser.add_argument(
+ "--topic", "-t",
+ required=True,
+ help="Market topic (e.g., 'Electric Vehicle Charging Infrastructure')"
+ )
+ parser.add_argument(
+ "--output-dir", "-o",
+ default="figures",
+ help="Output directory for generated images (default: figures)"
+ )
+ parser.add_argument(
+ "--all", "-a",
+ action="store_true",
+ help="Generate all 27 extended visuals (default: only core 5-6)"
+ )
+ parser.add_argument(
+ "--skip-existing", "-s",
+ action="store_true",
+ help="Skip generation if file already exists"
+ )
+ parser.add_argument(
+ "--verbose", "-v",
+ action="store_true",
+ help="Show detailed output"
+ )
+ parser.add_argument(
+ "--dry-run",
+ action="store_true",
+ help="Show what would be generated without actually generating"
+ )
+ parser.add_argument(
+ "--only",
+ type=str,
+ help="Only generate visuals matching this pattern (e.g., '01_', 'porter')"
+ )
+
+ args = parser.parse_args()
+
+ # Create output directory
+ output_dir = Path(args.output_dir)
+ if not args.dry_run:
+ output_dir.mkdir(parents=True, exist_ok=True)
+
+ print(f"\n{'='*60}")
+ print(f"Market Research Visual Generator")
+ print(f"{'='*60}")
+ print(f"Topic: {args.topic}")
+ print(f"Output Directory: {output_dir.absolute()}")
+ print(f"Mode: {'All Visuals (27)' if args.all else 'Core Visuals Only (5-6)'}")
+ print(f"Skip Existing: {args.skip_existing}")
+ print(f"{'='*60}\n")
+
+ # Select visual set based on --all flag
+ if args.all:
+ visuals_to_generate = CORE_VISUALS + EXTENDED_VISUALS
+ print("Generating ALL visuals (core + extended)\n")
+ else:
+ visuals_to_generate = CORE_VISUALS
+ print("Generating CORE visuals only (use --all for extended set)\n")
+
+ # Filter visuals if --only specified
+ if args.only:
+ pattern = args.only.lower()
+ visuals_to_generate = [
+ v for v in VISUALS
+ if pattern in v[0].lower() or pattern in v[2].lower()
+ ]
+ print(f"Filtered to {len(visuals_to_generate)} visuals matching '{args.only}'\n")
+
+ if args.dry_run:
+ print("DRY RUN - The following visuals would be generated:\n")
+ for filename, tool, prompt in visuals_to_generate:
+ formatted = prompt.format(topic=args.topic)
+ print(f" {filename}")
+ print(f" Tool: {tool}")
+ print(f" Prompt: {formatted[:60]}...")
+ print()
+ return
+
+ # Generate all visuals
+ total = len(visuals_to_generate)
+ success = 0
+ failed = 0
+ skipped = 0
+
+ for i, (filename, tool, prompt) in enumerate(visuals_to_generate, 1):
+ print(f"\n[{i}/{total}] Generating {filename}...")
+
+ result = generate_visual(
+ filename=filename,
+ tool=tool,
+ prompt=prompt,
+ output_dir=output_dir,
+ topic=args.topic,
+ skip_existing=args.skip_existing,
+ verbose=args.verbose
+ )
+
+ if result:
+ if args.skip_existing and (output_dir / filename).exists():
+ skipped += 1
+ else:
+ success += 1
+ else:
+ failed += 1
+
+ # Print summary
+ print(f"\n{'='*60}")
+ print(f"Generation Complete")
+ print(f"{'='*60}")
+ print(f"Total: {total}")
+ print(f"Success: {success}")
+ print(f"Skipped: {skipped}")
+ print(f"Failed: {failed}")
+ print(f"{'='*60}")
+
+ if failed > 0:
+ print(f"\nWARNING: {failed} visuals failed to generate.")
+ print("Check the output above for error details.")
+ print("You may need to generate failed visuals manually.")
+
+ print(f"\nOutput directory: {output_dir.absolute()}")
+
+
+if __name__ == "__main__":
+ main()
diff --git a/scientific-skills/paper-2-web/SKILL.md b/scientific-skills/paper-2-web/SKILL.md
new file mode 100644
index 0000000..8793722
--- /dev/null
+++ b/scientific-skills/paper-2-web/SKILL.md
@@ -0,0 +1,491 @@
+---
+name: paper-2-web
+description: This skill should be used when converting academic papers into promotional and presentation formats including interactive websites (Paper2Web), presentation videos (Paper2Video), and conference posters (Paper2Poster). Use this skill for tasks involving paper dissemination, conference preparation, creating explorable academic homepages, generating video abstracts, or producing print-ready posters from LaTeX or PDF sources.
+allowed-tools: [Read, Write, Edit, Bash]
+---
+
+# Paper2All: Academic Paper Transformation Pipeline
+
+## Overview
+
+This skill enables the transformation of academic papers into multiple promotional and presentation formats using the Paper2All autonomous pipeline. The system converts research papers (LaTeX or PDF) into three primary outputs:
+
+1. **Paper2Web**: Interactive, explorable academic homepages with layout-aware design
+2. **Paper2Video**: Professional presentation videos with narration, slides, and optional talking-head
+3. **Paper2Poster**: Print-ready conference posters with professional layouts
+
+The pipeline uses LLM-powered content extraction, design generation, and iterative refinement to create high-quality outputs suitable for conferences, journals, preprint repositories, and academic promotion.
+
+## When to Use This Skill
+
+Use this skill when:
+
+- **Creating conference materials**: Posters, presentation videos, and companion websites for academic conferences
+- **Promoting research**: Converting published papers or preprints into accessible, engaging web formats
+- **Preparing presentations**: Generating video abstracts or full presentation videos from paper content
+- **Disseminating findings**: Creating promotional materials for social media, lab websites, or institutional showcases
+- **Enhancing preprints**: Adding interactive homepages to bioRxiv, arXiv, or other preprint submissions
+- **Batch processing**: Generating promotional materials for multiple papers simultaneously
+
+**Trigger phrases**:
+- "Convert this paper to a website"
+- "Generate a conference poster from my LaTeX paper"
+- "Create a video presentation from this research"
+- "Make an interactive homepage for my paper"
+- "Transform my paper into promotional materials"
+- "Generate a poster and video for my conference talk"
+
+## Visual Enhancement with Scientific Schematics
+
+**When creating documents with this skill, always consider adding scientific diagrams and schematics to enhance visual communication.**
+
+If your document does not already contain schematics or diagrams:
+- Use the **scientific-schematics** skill to generate AI-powered publication-quality diagrams
+- Simply describe your desired diagram in natural language
+- Nano Banana Pro will automatically generate, review, and refine the schematic
+
+**For new documents:** Scientific schematics should be generated by default to visually represent key concepts, workflows, architectures, or relationships described in the text.
+
+**How to generate schematics:**
+```bash
+python scripts/generate_schematic.py "your diagram description" -o figures/output.png
+```
+
+The AI will automatically:
+- Create publication-quality images with proper formatting
+- Review and refine through multiple iterations
+- Ensure accessibility (colorblind-friendly, high contrast)
+- Save outputs in the figures/ directory
+
+**When to add schematics:**
+- Paper transformation pipeline diagrams
+- Website layout architecture diagrams
+- Video production workflow illustrations
+- Poster design process flowcharts
+- Content extraction diagrams
+- System architecture visualizations
+- Any complex concept that benefits from visualization
+
+For detailed guidance on creating schematics, refer to the scientific-schematics skill documentation.
+
+---
+
+## Core Capabilities
+
+### 1. Paper2Web: Interactive Website Generation
+
+Converts papers into layout-aware, interactive academic homepages that go beyond simple HTML conversion.
+
+**Key Features**:
+- Responsive, multi-section layouts adapted to paper content
+- Interactive figures, tables, and citations
+- Mobile-friendly design with navigation
+- Automatic logo discovery (with Google Search API)
+- Aesthetic refinement and quality assessment
+
+**Best For**: Post-publication promotion, preprint enhancement, lab websites, permanent research showcases
+
+→ **See `references/paper2web.md` for detailed documentation**
+
+---
+
+### 2. Paper2Video: Presentation Video Generation
+
+Generates professional presentation videos with slides, narration, cursor movements, and optional talking-head video.
+
+**Key Features**:
+- Automated slide generation from paper structure
+- Natural-sounding speech synthesis
+- Synchronized cursor movements and highlights
+- Optional talking-head video using Hallo2 (requires GPU)
+- Multi-language support
+
+**Best For**: Video abstracts, conference presentations, online talks, course materials, YouTube promotion
+
+→ **See `references/paper2video.md` for detailed documentation**
+
+---
+
+### 3. Paper2Poster: Conference Poster Generation
+
+Creates print-ready academic posters with professional layouts and visual design.
+
+**Key Features**:
+- Custom poster dimensions (any size)
+- Professional design templates
+- Institution branding support
+- QR code generation for links
+- High-resolution output (300+ DPI)
+
+**Best For**: Conference poster sessions, symposiums, academic exhibitions, virtual conferences
+
+→ **See `references/paper2poster.md` for detailed documentation**
+
+---
+
+## Quick Start
+
+### Prerequisites
+
+1. **Install Paper2All**:
+ ```bash
+ git clone https://github.com/YuhangChen1/Paper2All.git
+ cd Paper2All
+ conda create -n paper2all python=3.11
+ conda activate paper2all
+ pip install -r requirements.txt
+ ```
+
+2. **Configure API Keys** (create `.env` file):
+ ```
+ OPENAI_API_KEY=your_openai_api_key_here
+ # Optional: GOOGLE_API_KEY and GOOGLE_CSE_ID for logo search
+ ```
+
+3. **Install System Dependencies**:
+ - LibreOffice (document conversion)
+ - Poppler utilities (PDF processing)
+ - NVIDIA GPU with 48GB (optional, for talking-head videos)
+
+→ **See `references/installation.md` for complete installation guide**
+
+---
+
+### Basic Usage
+
+**Generate All Components** (website + poster + video):
+```bash
+python pipeline_all.py \
+ --input-dir "path/to/paper" \
+ --output-dir "path/to/output" \
+ --model-choice 1
+```
+
+**Generate Website Only**:
+```bash
+python pipeline_all.py \
+ --input-dir "path/to/paper" \
+ --output-dir "path/to/output" \
+ --model-choice 1 \
+ --generate-website
+```
+
+**Generate Poster with Custom Size**:
+```bash
+python pipeline_all.py \
+ --input-dir "path/to/paper" \
+ --output-dir "path/to/output" \
+ --model-choice 1 \
+ --generate-poster \
+ --poster-width-inches 60 \
+ --poster-height-inches 40
+```
+
+**Generate Video** (lightweight pipeline):
+```bash
+python pipeline_light.py \
+ --model_name_t gpt-4.1 \
+ --model_name_v gpt-4.1 \
+ --result_dir "path/to/output" \
+ --paper_latex_root "path/to/paper"
+```
+
+→ **See `references/usage_examples.md` for comprehensive workflow examples**
+
+---
+
+## Workflow Decision Tree
+
+Use this decision tree to determine which components to generate:
+
+```
+User needs promotional materials for paper?
+│
+├─ Need permanent online presence?
+│ └─→ Generate Paper2Web (interactive website)
+│
+├─ Need physical conference materials?
+│ ├─→ Poster session? → Generate Paper2Poster
+│ └─→ Oral presentation? → Generate Paper2Video
+│
+├─ Need video content?
+│ ├─→ Journal video abstract? → Generate Paper2Video (5-10 min)
+│ ├─→ Conference talk? → Generate Paper2Video (15-20 min)
+│ └─→ Social media? → Generate Paper2Video (1-3 min)
+│
+└─ Need complete package?
+ └─→ Generate all three components
+```
+
+## Input Requirements
+
+### Supported Input Formats
+
+**1. LaTeX Source** (Recommended):
+```
+paper_directory/
+├── main.tex # Main paper file
+├── sections/ # Optional: split sections
+├── figures/ # All figure files
+├── tables/ # Table files
+└── bibliography.bib # References
+```
+
+**2. PDF**:
+- High-quality PDF with embedded fonts
+- Selectable text (not scanned images)
+- High-resolution figures (300+ DPI preferred)
+
+### Input Organization
+
+**Single Paper**:
+```bash
+input/
+└── paper_name/
+ ├── main.tex (or paper.pdf)
+ ├── figures/
+ └── bibliography.bib
+```
+
+**Multiple Papers** (batch processing):
+```bash
+input/
+├── paper1/
+│ └── main.tex
+├── paper2/
+│ └── main.tex
+└── paper3/
+ └── main.tex
+```
+
+## Common Parameters
+
+### Model Selection
+- `--model-choice 1`: GPT-4 (best balance of quality and cost)
+- `--model-choice 2`: GPT-4.1 (latest features, higher cost)
+- `--model_name_t gpt-3.5-turbo`: Faster, lower cost (acceptable quality)
+
+### Component Selection
+- `--generate-website`: Enable website generation
+- `--generate-poster`: Enable poster generation
+- `--generate-video`: Enable video generation
+- `--enable-talking-head`: Add talking-head to video (requires GPU)
+
+### Customization
+- `--poster-width-inches [width]`: Custom poster width
+- `--poster-height-inches [height]`: Custom poster height
+- `--video-duration [seconds]`: Target video length
+- `--enable-logo-search`: Automatic institution logo discovery
+
+## Output Structure
+
+Generated outputs are organized by paper and component:
+
+```
+output/
+└── paper_name/
+ ├── website/
+ │ ├── index.html
+ │ ├── styles.css
+ │ └── assets/
+ ├── poster/
+ │ ├── poster_final.pdf
+ │ ├── poster_final.png
+ │ └── poster_source/
+ └── video/
+ ├── final_video.mp4
+ ├── slides/
+ ├── audio/
+ └── subtitles/
+```
+
+## Best Practices
+
+### Input Preparation
+1. **Use LaTeX when possible**: Provides best content extraction and structure
+2. **Organize files properly**: Keep all assets (figures, tables, bibliography) in paper directory
+3. **High-quality figures**: Use vector formats (PDF, SVG) or high-resolution rasters (300+ DPI)
+4. **Clean LaTeX**: Remove compilation artifacts, ensure source compiles successfully
+
+### Model Selection Strategy
+- **GPT-4**: Best for production-quality outputs, conferences, publications
+- **GPT-4.1**: Use when you need latest features or best possible quality
+- **GPT-3.5-turbo**: Use for quick drafts, testing, or simple papers
+
+### Component Priority
+For tight deadlines, generate in this order:
+1. **Website** (fastest, most versatile, ~15-30 min)
+2. **Poster** (moderate speed, for print deadlines, ~10-20 min)
+3. **Video** (slowest, can be generated later, ~20-60 min)
+
+### Quality Assurance
+Before finalizing outputs:
+1. **Website**: Test on multiple devices, verify all links work, check figure quality
+2. **Poster**: Print test page, verify text readability from 3-6 feet, check colors
+3. **Video**: Watch entire video, verify audio synchronization, test on different devices
+
+## Resource Requirements
+
+### Processing Time
+- **Website**: 15-30 minutes per paper
+- **Poster**: 10-20 minutes per paper
+- **Video (no talking-head)**: 20-60 minutes per paper
+- **Video (with talking-head)**: 60-120 minutes per paper
+
+### Computational Requirements
+- **CPU**: Multi-core processor for parallel processing
+- **RAM**: 16GB minimum, 32GB recommended for large papers
+- **GPU**: Optional for standard outputs, required for talking-head (NVIDIA A6000 48GB)
+- **Storage**: 1-5GB per paper depending on components and quality settings
+
+### API Costs (Approximate)
+- **Website**: $0.50-2.00 per paper (GPT-4)
+- **Poster**: $0.30-1.00 per paper (GPT-4)
+- **Video**: $1.00-3.00 per paper (GPT-4)
+- **Complete package**: $2.00-6.00 per paper (GPT-4)
+
+## Troubleshooting
+
+### Common Issues
+
+**LaTeX parsing errors**:
+- Ensure LaTeX source compiles successfully: `pdflatex main.tex`
+- Check all referenced files are present
+- Verify no custom packages prevent parsing
+
+**Poor figure quality**:
+- Use vector formats (PDF, SVG, EPS) instead of rasters
+- Ensure raster images are 300+ DPI
+- Check figures render correctly in compiled PDF
+
+**Video generation failures**:
+- Verify sufficient disk space (5GB+ recommended)
+- Check all dependencies installed (LibreOffice, Poppler)
+- Review error logs in output directory
+
+**Poster layout issues**:
+- Verify poster dimensions are reasonable (24"-72" range)
+- Check content length (very long papers may need manual curation)
+- Ensure figures have appropriate resolution for poster size
+
+**API errors**:
+- Verify API keys in `.env` file
+- Check API credit balance
+- Ensure no rate limiting (wait and retry)
+
+## Platform-Specific Features
+
+### Social Media Optimization
+
+The system auto-detects target platforms:
+
+**Twitter/X** (English, numeric folder names):
+```bash
+mkdir -p input/001_twitter/
+# Generates English promotional content
+```
+
+**Xiaohongshu/小红书** (Chinese, alphanumeric folder names):
+```bash
+mkdir -p input/xhs_paper/
+# Generates Chinese promotional content
+```
+
+### Conference-Specific Formatting
+
+Specify conference requirements:
+- Standard poster sizes (4'×3', 5'×4', A0, A1)
+- Video abstract length limits (typically 3-5 minutes)
+- Institution branding requirements
+- Color scheme preferences
+
+## Integration and Deployment
+
+### Website Deployment
+Deploy generated websites to:
+- **GitHub Pages**: Free hosting with custom domain
+- **Academic hosting**: University web servers
+- **Personal servers**: AWS, DigitalOcean, etc.
+- **Netlify/Vercel**: Modern hosting with CI/CD
+
+### Poster Printing
+Print-ready files work with:
+- Professional poster printing services
+- University print shops
+- Online services (e.g., Spoonflower, VistaPrint)
+- Large format printers (if available)
+
+### Video Distribution
+Share videos on:
+- **YouTube**: Public or unlisted for maximum reach
+- **Institutional repositories**: University video platforms
+- **Conference platforms**: Virtual conference systems
+- **Social media**: Twitter, LinkedIn, ResearchGate
+
+## Advanced Usage
+
+### Batch Processing
+Process multiple papers efficiently:
+```bash
+# Organize papers in batch directory
+for paper in paper1 paper2 paper3; do
+ python pipeline_all.py \
+ --input-dir input/$paper \
+ --output-dir output/$paper \
+ --model-choice 1 &
+done
+wait
+```
+
+### Custom Branding
+Apply institution or lab branding:
+- Provide logo files in paper directory
+- Specify color schemes in configuration
+- Use custom templates (advanced)
+- Match conference theme requirements
+
+### Multi-Language Support
+Generate content in different languages:
+- Specify target language in configuration
+- System translates content appropriately
+- Selects appropriate voice for video narration
+- Adapts design conventions to culture
+
+## References and Resources
+
+This skill includes comprehensive reference documentation:
+
+- **`references/installation.md`**: Complete installation and configuration guide
+- **`references/paper2web.md`**: Detailed Paper2Web documentation with all features
+- **`references/paper2video.md`**: Comprehensive Paper2Video guide including talking-head setup
+- **`references/paper2poster.md`**: Complete Paper2Poster documentation with design templates
+- **`references/usage_examples.md`**: Real-world examples and workflow patterns
+
+**External Resources**:
+- GitHub Repository: https://github.com/YuhangChen1/Paper2All
+- Curated Dataset: Available on Hugging Face (13 research categories)
+- Benchmark Suite: Reference websites and evaluation metrics
+
+## Evaluation and Quality Metrics
+
+The Paper2All system includes built-in quality assessment:
+
+### Content Quality
+- **Completeness**: Coverage of paper content
+- **Accuracy**: Faithful representation of findings
+- **Clarity**: Accessibility and understandability
+- **Informativeness**: Key information prominence
+
+### Design Quality
+- **Aesthetics**: Visual appeal and professionalism
+- **Layout**: Balance, hierarchy, and organization
+- **Readability**: Text legibility and figure clarity
+- **Consistency**: Uniform styling and branding
+
+### Technical Quality
+- **Performance**: Load times, responsiveness
+- **Compatibility**: Cross-browser, cross-device support
+- **Accessibility**: WCAG compliance, screen reader support
+- **Standards**: Valid HTML/CSS, print-ready PDFs
+
+All outputs undergo automated quality checks before generation completes.
diff --git a/scientific-skills/paper-2-web/references/installation.md b/scientific-skills/paper-2-web/references/installation.md
new file mode 100644
index 0000000..37dce01
--- /dev/null
+++ b/scientific-skills/paper-2-web/references/installation.md
@@ -0,0 +1,141 @@
+# Installation and Configuration
+
+## System Requirements
+
+### Hardware Requirements
+- **GPU**: NVIDIA A6000 (48GB minimum) required for video generation with talking-head features
+- **CPU**: Multi-core processor recommended for PDF processing and document conversion
+- **RAM**: 16GB minimum, 32GB recommended for large papers
+
+### Software Requirements
+- **Python**: 3.11 or higher
+- **Conda**: Environment manager for dependency isolation
+- **LibreOffice**: Required for document format conversion (PDF to PPTX, etc.)
+- **Poppler utilities**: Required for PDF processing and manipulation
+
+## Installation Steps
+
+### 1. Clone the Repository
+```bash
+git clone https://github.com/YuhangChen1/Paper2All.git
+cd Paper2All
+```
+
+### 2. Create Conda Environment
+```bash
+conda create -n paper2all python=3.11
+conda activate paper2all
+```
+
+### 3. Install Dependencies
+```bash
+pip install -r requirements.txt
+```
+
+### 4. Install System Dependencies
+
+**Ubuntu/Debian:**
+```bash
+sudo apt-get install libreoffice poppler-utils
+```
+
+**macOS:**
+```bash
+brew install libreoffice poppler
+```
+
+**Windows:**
+- Download and install LibreOffice from https://www.libreoffice.org/
+- Download and install Poppler from https://github.com/oschwartz10612/poppler-windows
+
+## API Configuration
+
+Create a `.env` file in the project root with the following credentials:
+
+### Required API Keys
+
+**Option 1: OpenAI API**
+```
+OPENAI_API_KEY=your_openai_api_key_here
+```
+
+**Option 2: OpenRouter API** (alternative to OpenAI)
+```
+OPENROUTER_API_KEY=your_openrouter_api_key_here
+```
+
+### Optional API Keys
+
+**Google Search API** (for automatic logo discovery)
+```
+GOOGLE_API_KEY=your_google_api_key_here
+GOOGLE_CSE_ID=your_custom_search_engine_id_here
+```
+
+## Model Configuration
+
+The system supports multiple LLM backends:
+
+### Supported Models
+- GPT-4 (recommended for best quality)
+- GPT-4.1 (latest version)
+- GPT-3.5-turbo (faster, lower cost)
+- Claude models via OpenRouter
+- Other OpenRouter-supported models
+
+### Model Selection
+
+Specify models using the `--model-choice` parameter or `--model_name_t` and `--model_name_v` parameters:
+- Model choice 1: GPT-4 for all components
+- Model choice 2: GPT-4.1 for all components
+- Custom: Specify separate models for text and visual processing
+
+## Verification
+
+Test the installation:
+
+```bash
+python pipeline_all.py --help
+```
+
+If successful, you should see the help menu with all available options.
+
+## Troubleshooting
+
+### Common Issues
+
+**1. LibreOffice not found**
+- Ensure LibreOffice is installed and in your system PATH
+- Try running `libreoffice --version` to verify
+
+**2. Poppler utilities not found**
+- Verify installation with `pdftoppm -v`
+- Add Poppler bin directory to PATH if needed
+
+**3. GPU/CUDA errors for video generation**
+- Ensure NVIDIA drivers are up to date
+- Verify CUDA toolkit is installed
+- Check GPU memory with `nvidia-smi`
+
+**4. API key errors**
+- Verify `.env` file is in the project root
+- Check that API keys are valid and have sufficient credits
+- Ensure no extra spaces or quotes around keys in `.env`
+
+## Directory Structure
+
+After installation, organize your workspace:
+
+```
+Paper2All/
+├── .env # API credentials
+├── input/ # Place your paper files here
+│ └── paper_name/ # Each paper in its own directory
+│ └── main.tex # LaTeX source or PDF
+├── output/ # Generated outputs
+│ └── paper_name/
+│ ├── website/ # Generated website files
+│ ├── video/ # Generated video files
+│ └── poster/ # Generated poster files
+└── ...
+```
diff --git a/scientific-skills/paper-2-web/references/paper2poster.md b/scientific-skills/paper-2-web/references/paper2poster.md
new file mode 100644
index 0000000..a7f22d2
--- /dev/null
+++ b/scientific-skills/paper-2-web/references/paper2poster.md
@@ -0,0 +1,346 @@
+# Paper2Poster: Academic Poster Generation
+
+## Overview
+
+Paper2Poster automatically generates professional academic posters from research papers. The system extracts key content, designs visually appealing layouts, and creates print-ready posters suitable for conferences, symposiums, and academic presentations.
+
+## Core Capabilities
+
+### 1. Content Extraction
+- Identifies key findings and contributions
+- Extracts important figures and tables
+- Summarizes methodology
+- Highlights results and conclusions
+- Preserves citations and references
+
+### 2. Layout Design
+- Creates balanced, professional layouts
+- Optimizes content density and white space
+- Establishes clear visual hierarchy
+- Supports multiple poster sizes
+- Adapts to different content types
+
+### 3. Visual Design
+- Applies color schemes and branding
+- Optimizes typography for readability
+- Ensures figure quality and sizing
+- Creates cohesive visual identity
+- Maintains academic presentation standards
+
+## Usage
+
+### Basic Poster Generation
+
+```bash
+python pipeline_all.py \
+ --input-dir "path/to/papers" \
+ --output-dir "path/to/output" \
+ --model-choice 1 \
+ --generate-poster
+```
+
+### Custom Poster Dimensions
+
+```bash
+python pipeline_all.py \
+ --input-dir "path/to/papers" \
+ --output-dir "path/to/output" \
+ --model-choice 2 \
+ --generate-poster \
+ --poster-width-inches 60 \
+ --poster-height-inches 40
+```
+
+### Parameters
+
+**Basic Configuration:**
+- `--input-dir`: Directory containing paper files
+- `--output-dir`: Directory for generated posters
+- `--model-choice`: LLM model selection (1=GPT-4, 2=GPT-4.1)
+- `--generate-poster`: Enable poster generation
+
+**Poster Dimensions:**
+- `--poster-width-inches`: Width in inches (default: 48)
+- `--poster-height-inches`: Height in inches (default: 36)
+- `--poster-orientation`: Portrait or landscape (default: landscape)
+- `--poster-dpi`: Resolution in DPI (default: 300)
+
+**Design Options:**
+- `--poster-template`: Template style (default: modern)
+- `--color-scheme`: Color palette selection
+- `--institution-branding`: Include institution colors and logos
+- `--font-family`: Typography selection
+
+## Standard Poster Sizes
+
+### Conference Standard Sizes
+- **4' × 3'** (48" × 36"): Most common conference poster
+- **5' × 4'** (60" × 48"): Large format for major conferences
+- **3' × 4'** (36" × 48"): Portrait orientation for narrow spaces
+- **A0** (841mm × 1189mm): International standard
+- **A1** (594mm × 841mm): Compact conference poster
+
+### Custom Sizes
+The system supports any custom dimensions. Specify using:
+```bash
+--poster-width-inches [width] --poster-height-inches [height]
+```
+
+## Input Requirements
+
+### Supported Input Formats
+1. **LaTeX source** (preferred)
+ - Main `.tex` file with complete paper
+ - All figures and tables referenced
+ - Compiled successfully
+
+2. **PDF**
+ - High-quality PDF with embedded fonts
+ - Selectable text (not scanned)
+ - High-resolution figures
+
+### Required Content Elements
+- Title and authors
+- Abstract or summary
+- Methodology description
+- Key results
+- Conclusions
+- References (optional but recommended)
+
+### Recommended Assets
+- High-resolution figures (300 DPI minimum)
+- Vector graphics (PDF, SVG, EPS)
+- Institution logo
+- Author photos (optional)
+- QR codes for website/repo links
+
+## Output Structure
+
+```
+output/paper_name/poster/
+├── poster_final.pdf # Print-ready poster
+├── poster_final.png # High-res PNG version
+├── poster_preview.pdf # Low-res preview
+├── poster_source/ # Source files
+│ ├── layout.pptx # Editable PowerPoint
+│ ├── layout.svg # Vector graphics
+│ └── layout.json # Layout specification
+├── assets/ # Extracted assets
+│ ├── figures/ # Poster figures
+│ ├── logos/ # Institution logos
+│ └── qrcodes/ # Generated QR codes
+└── metadata/
+ ├── design_spec.json # Design specifications
+ └── content_map.json # Content organization
+```
+
+## Poster Layout Sections
+
+### Standard Sections
+1. **Header**
+ - Title (large, prominent)
+ - Authors and affiliations
+ - Institution logos
+ - Conference information
+
+2. **Introduction/Background**
+ - Problem statement
+ - Research motivation
+ - Brief literature context
+
+3. **Methods**
+ - Experimental design
+ - Key procedures
+ - Important parameters
+ - Visual workflow diagram
+
+4. **Results**
+ - Key findings (largest section)
+ - Primary figures and tables
+ - Statistical summaries
+ - Visual data representations
+
+5. **Conclusions**
+ - Main takeaways
+ - Implications
+ - Future work
+
+6. **References & Contact**
+ - Selected key references
+ - Author contact information
+ - QR codes for paper/website
+ - Acknowledgments
+
+## Design Templates
+
+### Modern Template (Default)
+- Clean, minimalist design
+- Bold colors for headers
+- Ample white space
+- Modern typography
+- Focus on visual hierarchy
+
+### Academic Template
+- Traditional academic styling
+- Conservative color palette
+- Dense information layout
+- Classic serif typography
+- Standard section organization
+
+### Visual Template
+- Image-focused layout
+- Large figure displays
+- Minimal text density
+- Infographic elements
+- Story-driven flow
+
+### Technical Template
+- Equation-friendly layout
+- Code snippet support
+- Detailed methodology sections
+- Technical figure emphasis
+- Engineering/CS aesthetic
+
+## Color Schemes
+
+### Predefined Schemes
+- **Institutional**: Uses institution branding colors
+- **Professional**: Navy blue and gray palette
+- **Vibrant**: Bold, eye-catching colors
+- **Nature**: Green and earth tones
+- **Tech**: Modern blue and cyan
+- **Warm**: Orange and red accents
+- **Cool**: Blue and purple tones
+
+### Custom Color Schemes
+Specify custom colors in configuration:
+```json
+{
+ "primary": "#1E3A8A",
+ "secondary": "#3B82F6",
+ "accent": "#F59E0B",
+ "background": "#FFFFFF",
+ "text": "#1F2937"
+}
+```
+
+## Typography Options
+
+### Font Families
+- **Sans-serif** (default): Clean, modern, highly readable
+- **Serif**: Traditional academic appearance
+- **Mixed**: Serif for body, sans-serif for headers
+- **Monospace**: For code and technical content
+
+### Size Hierarchy
+- **Title**: 72-96pt
+- **Section headers**: 48-60pt
+- **Subsection headers**: 36-48pt
+- **Body text**: 24-32pt
+- **Captions**: 18-24pt
+- **References**: 16-20pt
+
+## Quality Assurance
+
+### Automated Checks
+- **Text readability**: Minimum font size verification
+- **Color contrast**: Accessibility compliance
+- **Figure quality**: Resolution and clarity checks
+- **Layout balance**: Content distribution analysis
+- **Branding consistency**: Logo and color verification
+
+### Manual Review Checklist
+1. ☐ All figures are high resolution and clear
+2. ☐ Text is readable from 3-6 feet away
+3. ☐ Color scheme is professional and consistent
+4. ☐ No text overlaps or layout issues
+5. ☐ Institution logos are correct and high quality
+6. ☐ QR codes work and link to correct URLs
+7. ☐ Author information is accurate
+8. ☐ Key findings are prominently displayed
+9. ☐ References are properly formatted
+10. ☐ File is correct size and resolution for printing
+
+## Print Preparation
+
+### File Specifications
+- **Format**: PDF/X-1a or PDF/X-4 for professional printing
+- **Resolution**: 300 DPI minimum, 600 DPI for fine details
+- **Color mode**: CMYK for print (system auto-converts from RGB)
+- **Bleed**: 0.125" bleed on all sides (automatically added)
+- **Fonts**: All fonts embedded in PDF
+
+### Printing Recommendations
+1. **Print shop**: Use professional poster printing service
+2. **Paper type**: Matte or satin finish for academic posters
+3. **Backing**: Foam core or rigid backing for stability
+4. **Protection**: Lamination optional but recommended
+5. **Test print**: Print A4/Letter size preview first
+
+### Budget Options
+- **Standard**: $50-100 for 4'×3' poster at professional shop
+- **Economy**: $20-40 for print-only (no mounting)
+- **Premium**: $150-300 for high-end materials and mounting
+- **DIY**: <$10 for multiple pages tiled and assembled
+
+## Advanced Features
+
+### QR Code Generation
+Automatically generates QR codes for:
+- Paper PDF or DOI
+- Project website
+- GitHub repository
+- Data repository
+- Author profiles (ORCID, Google Scholar)
+
+### Institution Branding
+When enabled:
+- Extracts institution from author affiliations
+- Searches for official logos (requires Google Search API)
+- Applies institution color schemes
+- Matches brand guidelines
+
+### Interactive Elements (Digital Posters)
+For digital display or virtual conferences:
+- Clickable links and references
+- Embedded videos in figures
+- Interactive data visualizations
+- Animated transitions
+
+## Best Practices
+
+### Content Optimization
+1. **Focus on key findings**: Poster should tell story at a glance
+2. **Limit text**: Use bullet points, avoid paragraphs
+3. **Prioritize visuals**: Figures should dominate the space
+4. **Clear flow**: Guide viewer through logical progression
+5. **Highlight contributions**: Make novelty obvious
+
+### Design Optimization
+1. **Use contrast**: Ensure text is easily readable
+2. **Maintain hierarchy**: Size indicates importance
+3. **Balance content**: Avoid crowding any section
+4. **Consistent styling**: Same fonts, colors throughout
+5. **White space**: Don't fill every inch
+
+### Figure Optimization
+1. **Large enough**: Minimum 6" width for main figures
+2. **High resolution**: 300 DPI minimum
+3. **Clear labels**: Axis labels, legends readable
+4. **Remove clutter**: Simplify for poster format
+5. **Use captions**: Brief, informative descriptions
+
+## Limitations
+
+- Complex equations may need manual adjustment for readability
+- Very long papers may require content prioritization
+- Custom branding requires manual specification or API access
+- Multi-language support limited to common languages
+- 3D visualizations may lose quality in 2D poster format
+
+## Integration with Other Components
+
+Combine Paper2Poster with:
+- **Paper2Web**: Use matching visual design and color scheme
+- **Paper2Video**: Create poster walk-through video
+- **AutoPR**: Generate social media graphics from poster
diff --git a/scientific-skills/paper-2-web/references/paper2video.md b/scientific-skills/paper-2-web/references/paper2video.md
new file mode 100644
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--- /dev/null
+++ b/scientific-skills/paper-2-web/references/paper2video.md
@@ -0,0 +1,305 @@
+# Paper2Video: Presentation Video Generation
+
+## Overview
+
+Paper2Video generates presentation videos from LaTeX sources, transforming academic papers into engaging video presentations. The system processes papers through multiple specialized modules to create professional presentation videos complete with slides, narration, and optional talking-head video.
+
+## Core Components
+
+### 1. Slide Generation Module
+- Extracts key content from paper structure
+- Creates visually appealing presentation slides
+- Organizes content in logical flow
+- Includes figures, tables, and equations
+- Optimizes text density for readability
+
+### 2. Subtitle Generation Module
+- Generates natural presentation script
+- Synchronizes text with slide transitions
+- Creates speaker notes and timing
+- Supports multiple languages
+- Optimizes for speech synthesis
+
+### 3. Speech Synthesis Module
+- Converts subtitles to natural-sounding speech
+- Supports multiple voices and accents
+- Controls pacing and emphasis
+- Generates audio track for video
+- Handles technical terminology
+
+### 4. Cursor Movement Module
+- Simulates presenter cursor movements
+- Highlights key points on slides
+- Guides viewer attention
+- Creates natural presentation flow
+- Synchronizes with narration
+
+### 5. Talking-Head Video Generation (Optional)
+- Uses Hallo2 for realistic presenter video
+- Lip-syncs with generated audio
+- Requires reference image or video
+- GPU-intensive (NVIDIA A6000 48GB minimum)
+- Creates engaging presenter presence
+
+## Usage
+
+### Basic Video Generation (Without Talking-Head)
+
+```bash
+python pipeline_light.py \
+ --model_name_t gpt-4.1 \
+ --model_name_v gpt-4.1 \
+ --result_dir /path/to/output \
+ --paper_latex_root /path/to/paper
+```
+
+### Full Video Generation (With Talking-Head)
+
+```bash
+python pipeline_all.py \
+ --input-dir "path/to/papers" \
+ --output-dir "path/to/output" \
+ --model-choice 1 \
+ --enable-talking-head
+```
+
+### Parameters
+
+**Model Configuration:**
+- `--model_name_t`: Model for text/subtitle generation (default: gpt-4.1)
+- `--model_name_v`: Model for visual/slide generation (default: gpt-4.1)
+- `--model-choice`: Preset model configuration (1=GPT-4, 2=GPT-4.1)
+
+**Input/Output:**
+- `--paper_latex_root`: Root directory of LaTeX paper source
+- `--result_dir` or `--output-dir`: Output directory for generated videos
+- `--input-dir`: Directory containing multiple papers to process
+
+**Video Options:**
+- `--enable-talking-head`: Enable talking-head video generation (requires GPU)
+- `--video-duration`: Target video duration in seconds (default: auto-calculated)
+- `--slides-per-minute`: Control presentation pacing (default: 2-3)
+- `--voice`: Voice selection for speech synthesis
+
+**Quality Settings:**
+- `--video-resolution`: Output resolution (default: 1920x1080)
+- `--video-fps`: Frame rate (default: 30)
+- `--audio-quality`: Audio bitrate (default: 192kbps)
+
+## Input Requirements
+
+### LaTeX Source Structure
+```
+paper_directory/
+├── main.tex # Main paper file
+├── sections/ # Section files (if split)
+│ ├── introduction.tex
+│ ├── methods.tex
+│ └── results.tex
+├── figures/ # Figure files
+│ ├── fig1.pdf
+│ ├── fig2.png
+│ └── ...
+├── tables/ # Table files
+└── bibliography.bib # References
+```
+
+### Required Elements
+- Valid LaTeX source that compiles
+- Proper section structure (abstract, introduction, methods, results, conclusion)
+- High-quality figures (vector formats preferred)
+- Complete bibliography
+
+### Optional Elements
+- Author photos for talking-head generation
+- Custom slide templates
+- Background music or sound effects
+- Institution branding assets
+
+## Output Structure
+
+```
+output/paper_name/video/
+├── final_video.mp4 # Complete presentation video
+├── slides/ # Generated slide images
+│ ├── slide_001.png
+│ ├── slide_002.png
+│ └── ...
+├── audio/ # Audio components
+│ ├── narration.mp3 # Speech synthesis output
+│ └── background.mp3 # Optional background audio
+├── subtitles/ # Subtitle files
+│ ├── subtitles.srt # Standard subtitle format
+│ └── subtitles.vtt # WebVTT format
+├── script/ # Presentation script
+│ ├── full_script.txt # Complete narration text
+│ └── slide_notes.json # Slide-by-slide notes
+└── metadata/ # Video metadata
+ ├── timings.json # Slide timing information
+ └── video_info.json # Video properties
+```
+
+## Video Generation Process
+
+### Phase 1: Content Analysis
+1. Parse LaTeX source structure
+2. Extract key concepts and findings
+3. Identify important figures and equations
+4. Determine logical presentation flow
+
+### Phase 2: Slide Creation
+1. Design slide layouts based on content
+2. Allocate content across appropriate number of slides
+3. Incorporate figures and visual elements
+4. Apply consistent styling and branding
+
+### Phase 3: Script Generation
+1. Write natural presentation narration
+2. Time script sections to slides
+3. Add transitions and emphasis
+4. Optimize for speech synthesis
+
+### Phase 4: Audio Production
+1. Generate speech from script
+2. Add emphasis and pacing
+3. Include pauses for slide transitions
+4. Mix with optional background audio
+
+### Phase 5: Video Assembly
+1. Combine slides with timing information
+2. Synchronize audio track
+3. Add cursor movements and highlights
+4. Generate talking-head video (if enabled)
+5. Render final video file
+
+## Customization Options
+
+### Presentation Style
+- **Academic**: Formal, detailed, comprehensive
+- **Conference**: Focused on key findings, faster pace
+- **Public**: Simplified language, engaging storytelling
+- **Tutorial**: Step-by-step explanation, educational focus
+
+### Voice Configuration
+Available voice options (via speech synthesis):
+- Multiple languages and accents
+- Male/female voice selection
+- Speaking rate adjustment
+- Pitch and tone customization
+
+### Visual Themes
+- Institution branding colors
+- Conference template matching
+- Custom backgrounds and fonts
+- Dark mode presentations
+
+## Quality Assessment
+
+### Content Quality Metrics
+- **Completeness**: Coverage of paper content
+- **Clarity**: Explanation quality and coherence
+- **Flow**: Logical progression of ideas
+- **Engagement**: Visual appeal and pacing
+
+### Technical Quality Metrics
+- **Audio quality**: Speech clarity and naturalness
+- **Video quality**: Resolution and encoding
+- **Synchronization**: Audio-visual alignment
+- **Timing**: Appropriate slide duration
+
+## Advanced Features
+
+### Multi-Language Support
+- Generate presentations in multiple languages
+- Automatic translation of script
+- Language-appropriate voice selection
+- Cultural adaptation of presentation style
+
+### Talking-Head Generation with Hallo2
+Requires:
+- NVIDIA A6000 GPU (48GB minimum)
+- Reference image or short video of presenter
+- Additional processing time (2-3x longer)
+
+Benefits:
+- More engaging presentation
+- Professional presenter appearance
+- Natural gestures and expressions
+- Lip-sync accuracy
+
+### Interactive Elements
+- Embedded clickable links
+- Navigation menu
+- Chapter markers
+- Supplementary material links
+
+## Best Practices
+
+### Input Preparation
+1. **Clean LaTeX source**: Remove unnecessary comments and artifacts
+2. **High-quality figures**: Use vector formats when possible
+3. **Clear structure**: Well-organized sections and subsections
+4. **Complete content**: Include all necessary files and references
+
+### Model Selection
+- **Text generation (model_name_t)**: GPT-4.1 for best script quality
+- **Visual generation (model_name_v)**: GPT-4.1 for optimal slide design
+- For faster processing with acceptable quality: GPT-3.5-turbo
+
+### Video Optimization
+1. **Target duration**: 10-15 minutes for conference talks, 30-45 for detailed presentations
+2. **Pacing**: 2-3 slides per minute for technical content
+3. **Resolution**: 1920x1080 for standard, 3840x2160 for high-quality
+4. **Audio**: 192kbps minimum for clear speech
+
+### Quality Review
+Before finalizing:
+1. Watch entire video for content accuracy
+2. Check audio synchronization with slides
+3. Verify figure quality and readability
+4. Test subtitle accuracy and timing
+5. Review cursor movements for natural flow
+
+## Performance Considerations
+
+### Processing Time
+- **Without talking-head**: 10-30 minutes per paper (depending on length)
+- **With talking-head**: 30-120 minutes per paper
+- **Factors**: Paper length, figure count, model speed, GPU availability
+
+### Resource Requirements
+- **CPU**: Multi-core recommended for parallel processing
+- **RAM**: 16GB minimum, 32GB for large papers
+- **GPU**: Optional for standard, required for talking-head (A6000 48GB)
+- **Storage**: 1-5GB per video depending on length and quality
+
+## Troubleshooting
+
+### Common Issues
+
+**1. LaTeX parsing errors**
+- Ensure LaTeX source compiles successfully
+- Check for special packages or custom commands
+- Verify all referenced files are present
+
+**2. Speech synthesis problems**
+- Check audio quality settings
+- Verify text is properly formatted
+- Test with different voice options
+
+**3. Video rendering failures**
+- Check available disk space
+- Verify all dependencies are installed
+- Review error logs for specific issues
+
+**4. Talking-head generation errors**
+- Confirm GPU memory (48GB required)
+- Check CUDA drivers are up to date
+- Verify reference image quality and format
+
+## Integration with Other Components
+
+Combine Paper2Video with:
+- **Paper2Web**: Embed video in generated website
+- **Paper2Poster**: Use matching visual style
+- **AutoPR**: Create promotional clips from full video
diff --git a/scientific-skills/paper-2-web/references/paper2web.md b/scientific-skills/paper-2-web/references/paper2web.md
new file mode 100644
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@@ -0,0 +1,187 @@
+# Paper2Web: Academic Homepage Generation
+
+## Overview
+
+Paper2Web converts academic papers into interactive, explorable academic homepages. Unlike traditional approaches (direct generation, template-based, or HTML conversion), Paper2Web creates layout-aware, interactive websites through an iterative refinement process.
+
+## Core Capabilities
+
+### 1. Layout-Aware Generation
+- Analyzes paper structure and content organization
+- Creates responsive, multi-section layouts
+- Adapts design based on paper type (research article, review, preprint, etc.)
+
+### 2. Interactive Elements
+- Expandable sections for detailed content
+- Interactive figures and tables
+- Embedded citations and references
+- Navigation menu for easy browsing
+- Mobile-responsive design
+
+### 3. Content Refinement
+The system uses an iterative pipeline:
+1. Initial content extraction and structuring
+2. Layout generation with visual hierarchy
+3. Interactive element integration
+4. Aesthetic refinement
+5. Quality assessment and validation
+
+## Usage
+
+### Basic Website Generation
+
+```bash
+python pipeline_all.py \
+ --input-dir "path/to/papers" \
+ --output-dir "path/to/output" \
+ --model-choice 1
+```
+
+### Parameters
+
+- `--input-dir`: Directory containing paper files (PDF or LaTeX)
+- `--output-dir`: Directory for generated website files
+- `--model-choice`: LLM model selection (1=GPT-4, 2=GPT-4.1)
+- `--enable-logo-search`: Use Google Search API to find institution logos (optional)
+
+### Input Format Requirements
+
+**Supported Input Formats:**
+1. **LaTeX source** (preferred for best results)
+ - Main file: `main.tex`
+ - Include all referenced figures, tables, and bibliography files
+ - Organize in a single directory per paper
+
+2. **PDF files**
+ - High-quality PDF with selectable text
+ - Embedded figures should be high resolution
+ - Proper section headers and structure
+
+**Directory Structure:**
+```
+input/
+└── paper_name/
+ ├── main.tex # LaTeX source
+ ├── bibliography.bib # References
+ ├── figures/ # Figure files
+ │ ├── fig1.png
+ │ └── fig2.pdf
+ └── tables/ # Table files
+```
+
+## Output Structure
+
+Generated websites include:
+
+```
+output/paper_name/website/
+├── index.html # Main webpage
+├── styles.css # Styling
+├── script.js # Interactive features
+├── assets/ # Images and media
+│ ├── figures/
+│ └── logos/
+└── data/ # Structured data (optional)
+```
+
+## Customization Options
+
+### Visual Design
+The generated websites automatically include:
+- Professional color schemes based on paper content
+- Typography optimized for readability
+- Consistent spacing and visual hierarchy
+- Dark mode support (optional)
+
+### Content Sections
+Standard sections include:
+- Abstract
+- Key findings/contributions
+- Methodology overview
+- Results and visualizations
+- Discussion and implications
+- References and citations
+- Author information and affiliations
+
+Additional sections are automatically added based on paper content:
+- Code repositories
+- Dataset links
+- Supplementary materials
+- Related publications
+
+## Quality Assessment
+
+Paper2Web includes built-in evaluation:
+
+### Aesthetic Metrics
+- Layout balance and spacing
+- Color harmony
+- Typography consistency
+- Visual hierarchy effectiveness
+
+### Informativeness Metrics
+- Content completeness
+- Key finding clarity
+- Method explanation adequacy
+- Results presentation quality
+
+### Technical Metrics
+- Page load time
+- Mobile responsiveness
+- Browser compatibility
+- Accessibility compliance
+
+## Advanced Features
+
+### Logo Discovery
+When enabled with Google Search API:
+- Automatically finds institution logos
+- Matches author affiliations
+- Downloads and optimizes logo images
+- Integrates into website header
+
+### Citation Integration
+- Interactive reference list
+- Hover previews for citations
+- Links to DOI and external sources
+- Citation count tracking (if available)
+
+### Figure Enhancement
+- High-resolution figure rendering
+- Zoom and pan functionality
+- Caption and description integration
+- Multi-panel figure navigation
+
+## Best Practices
+
+### Input Preparation
+1. **Use LaTeX when possible**: Provides best structure extraction
+2. **Include all assets**: Figures, tables, and bibliography files
+3. **Clean formatting**: Remove compilation artifacts and temporary files
+4. **High-quality figures**: Use vector formats (PDF, SVG) when available
+
+### Model Selection
+- **GPT-4**: Best balance of quality and cost
+- **GPT-4.1**: Latest features, higher cost
+- **GPT-3.5-turbo**: Faster processing, acceptable for simple papers
+
+### Output Optimization
+1. Review generated content for accuracy
+2. Check that all figures render correctly
+3. Test interactive elements functionality
+4. Verify mobile responsiveness
+5. Validate external links
+
+## Limitations
+
+- Complex mathematical equations may require manual review
+- Multi-column layouts in PDF may affect extraction quality
+- Large papers (>50 pages) may require extended processing time
+- Some specialized figure types may need manual adjustment
+
+## Integration with Other Components
+
+Paper2Web can be combined with:
+- **Paper2Video**: Generate companion video for the website
+- **Paper2Poster**: Create matching poster design
+- **AutoPR**: Generate promotional content linking to website
diff --git a/scientific-skills/paper-2-web/references/usage_examples.md b/scientific-skills/paper-2-web/references/usage_examples.md
new file mode 100644
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+++ b/scientific-skills/paper-2-web/references/usage_examples.md
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+# Usage Examples and Workflows
+
+## Complete Workflow Examples
+
+### Example 1: Conference Presentation Package
+
+**Scenario**: Preparing for a major conference presentation with website, poster, and video.
+
+**User Request**: "I need to create a complete presentation package for my NeurIPS paper submission. Generate a website, poster, and video presentation."
+
+**Workflow**:
+
+```bash
+# Step 1: Organize paper files
+mkdir -p input/neurips2025_paper
+cp main.tex input/neurips2025_paper/
+cp -r figures/ input/neurips2025_paper/
+cp -r tables/ input/neurips2025_paper/
+cp bibliography.bib input/neurips2025_paper/
+
+# Step 2: Generate all components
+python pipeline_all.py \
+ --input-dir input/neurips2025_paper \
+ --output-dir output/ \
+ --model-choice 1 \
+ --generate-website \
+ --generate-poster \
+ --generate-video \
+ --poster-width-inches 48 \
+ --poster-height-inches 36 \
+ --enable-logo-search
+
+# Step 3: Review outputs
+ls -R output/neurips2025_paper/
+# - website/index.html
+# - poster/poster_final.pdf
+# - video/final_video.mp4
+```
+
+**Output**:
+- Interactive website showcasing research
+- 4'×3' conference poster (print-ready)
+- 12-minute presentation video
+- Processing time: ~45 minutes (without talking-head)
+
+---
+
+### Example 2: Quick Website for Preprint
+
+**Scenario**: Creating an explorable homepage for a bioRxiv preprint.
+
+**User Request**: "Convert my genomics preprint to an interactive website to accompany the bioRxiv submission."
+
+**Workflow**:
+
+```bash
+# Using PDF input (LaTeX not available)
+python pipeline_all.py \
+ --input-dir papers/genomics_preprint/ \
+ --output-dir output/genomics_web/ \
+ --model-choice 1 \
+ --generate-website
+
+# Deploy to GitHub Pages or personal server
+cd output/genomics_web/website/
+# Add link to bioRxiv paper, data repositories, code
+# Upload to hosting service
+```
+
+**Tips**:
+- Include links to bioRxiv DOI
+- Add GitHub repository links
+- Include data availability section
+- Embed interactive visualizations if possible
+
+---
+
+### Example 3: Video Abstract for Journal Submission
+
+**Scenario**: Creating a video abstract for a journal that encourages multimedia submissions.
+
+**User Request**: "Generate a 5-minute video abstract for my Nature Communications submission."
+
+**Workflow**:
+
+```bash
+# Generate concise video focusing on key findings
+python pipeline_light.py \
+ --model_name_t gpt-4.1 \
+ --model_name_v gpt-4.1 \
+ --result_dir output/video_abstract/ \
+ --paper_latex_root papers/nature_comms/ \
+ --video-duration 300 \
+ --slides-per-minute 3
+
+# Optional: Add custom intro/outro slides
+# Optional: Include talking-head for introduction
+```
+
+**Output**:
+- 5-minute video abstract
+- Focus on visual results
+- Clear, accessible narration
+- Journal-ready format
+
+---
+
+### Example 4: Multi-Paper Website Generation
+
+**Scenario**: Creating websites for multiple papers from a research group.
+
+**User Request**: "Generate websites for all 5 papers our lab published this year."
+
+**Workflow**:
+
+```bash
+# Organize papers
+mkdir -p batch_input/
+# Create subdirectories: paper1/, paper2/, paper3/, paper4/, paper5/
+# Each with their LaTeX sources
+
+# Batch process
+python pipeline_all.py \
+ --input-dir batch_input/ \
+ --output-dir batch_output/ \
+ --model-choice 1 \
+ --generate-website \
+ --enable-logo-search
+
+# Creates:
+# batch_output/paper1/website/
+# batch_output/paper2/website/
+# batch_output/paper3/website/
+# batch_output/paper4/website/
+# batch_output/paper5/website/
+```
+
+**Best Practice**:
+- Use consistent naming conventions
+- Process overnight for large batches
+- Review each website for accuracy
+- Deploy to unified lab website
+
+---
+
+### Example 5: Poster for Virtual Conference
+
+**Scenario**: Creating a digital poster for a virtual conference with interactive elements.
+
+**User Request**: "Create a poster for the virtual ISMB conference with clickable links to code and data."
+
+**Workflow**:
+
+```bash
+# Generate poster with QR codes and links
+python pipeline_all.py \
+ --input-dir papers/ismb_submission/ \
+ --output-dir output/ismb_poster/ \
+ --model-choice 1 \
+ --generate-poster \
+ --poster-width-inches 48 \
+ --poster-height-inches 36 \
+ --enable-qr-codes
+
+# Manually add QR codes to:
+# - GitHub repository
+# - Interactive results dashboard
+# - Supplementary data
+# - Video presentation
+```
+
+**Digital Enhancements**:
+- PDF with embedded hyperlinks
+- High-resolution PNG for virtual platform
+- Separate PDF with video links for download
+
+---
+
+### Example 6: Promotional Video Clip
+
+**Scenario**: Creating a short promotional video for social media.
+
+**User Request**: "Generate a 2-minute highlight video of our Cell paper for Twitter."
+
+**Workflow**:
+
+```bash
+# Generate short, engaging video
+python pipeline_light.py \
+ --model_name_t gpt-4.1 \
+ --model_name_v gpt-4.1 \
+ --result_dir output/promo_video/ \
+ --paper_latex_root papers/cell_paper/ \
+ --video-duration 120 \
+ --presentation-style public
+
+# Post-process:
+# - Extract key 30-second clip for Twitter
+# - Add captions for sound-off viewing
+# - Optimize file size for social media
+```
+
+**Social Media Optimization**:
+- Square format (1:1) for Instagram
+- Horizontal format (16:9) for Twitter/LinkedIn
+- Vertical format (9:16) for TikTok/Stories
+- Add text overlays for key findings
+
+---
+
+## Common Use Case Patterns
+
+### Pattern 1: LaTeX Paper → Full Package
+
+**Input**: LaTeX source with all assets
+**Output**: Website + Poster + Video
+**Time**: 45-90 minutes
+**Best for**: Major publications, conference presentations
+
+```bash
+python pipeline_all.py \
+ --input-dir [latex_dir] \
+ --output-dir [output_dir] \
+ --model-choice 1 \
+ --generate-website \
+ --generate-poster \
+ --generate-video
+```
+
+---
+
+### Pattern 2: PDF → Interactive Website
+
+**Input**: Published PDF paper
+**Output**: Explorable website
+**Time**: 15-30 minutes
+**Best for**: Post-publication promotion, preprint enhancement
+
+```bash
+python pipeline_all.py \
+ --input-dir [pdf_dir] \
+ --output-dir [output_dir] \
+ --model-choice 1 \
+ --generate-website
+```
+
+---
+
+### Pattern 3: LaTeX → Conference Poster
+
+**Input**: LaTeX paper
+**Output**: Print-ready poster (custom size)
+**Time**: 10-20 minutes
+**Best for**: Conference poster sessions
+
+```bash
+python pipeline_all.py \
+ --input-dir [latex_dir] \
+ --output-dir [output_dir] \
+ --model-choice 1 \
+ --generate-poster \
+ --poster-width-inches [width] \
+ --poster-height-inches [height]
+```
+
+---
+
+### Pattern 4: LaTeX → Presentation Video
+
+**Input**: LaTeX paper
+**Output**: Narrated presentation video
+**Time**: 20-60 minutes (without talking-head)
+**Best for**: Video abstracts, online presentations, course materials
+
+```bash
+python pipeline_light.py \
+ --model_name_t gpt-4.1 \
+ --model_name_v gpt-4.1 \
+ --result_dir [output_dir] \
+ --paper_latex_root [latex_dir]
+```
+
+---
+
+## Platform-Specific Outputs
+
+### Twitter/X Promotional Content
+
+The system auto-detects Twitter targeting for numeric folder names:
+
+```bash
+# Create Twitter-optimized content
+mkdir -p input/001_twitter_post/
+# System generates English promotional content
+```
+
+**Generated Output**:
+- Short, engaging summary
+- Key figure highlights
+- Hashtag recommendations
+- Thread-ready format
+
+---
+
+### Xiaohongshu (小红书) Content
+
+For Chinese social media, use alphanumeric folder names:
+
+```bash
+# Create Xiaohongshu-optimized content
+mkdir -p input/xhs_genomics/
+# System generates Chinese promotional content
+```
+
+**Generated Output**:
+- Chinese language content
+- Platform-appropriate formatting
+- Visual-first presentation
+- Engagement optimizations
+
+---
+
+## Troubleshooting Common Scenarios
+
+### Scenario: Large Paper (>50 pages)
+
+**Challenge**: Processing time and content selection
+**Solution**:
+```bash
+# Option 1: Focus on key sections
+# Edit LaTeX to comment out less critical sections
+
+# Option 2: Process in parts
+# Generate website for overview
+# Generate separate detailed videos for methods/results
+
+# Option 3: Use faster model for initial pass
+# Review and regenerate critical components with better model
+```
+
+---
+
+### Scenario: Complex Mathematical Content
+
+**Challenge**: Equations may not render perfectly
+**Solution**:
+- Use LaTeX input (not PDF) for best equation handling
+- Review generated content for equation accuracy
+- Manually adjust complex equations if needed
+- Consider using figure screenshots for critical equations
+
+---
+
+### Scenario: Non-Standard Paper Structure
+
+**Challenge**: Paper doesn't follow standard IMRAD format
+**Solution**:
+- Provide custom section guidance in paper metadata
+- Review generated structure and adjust
+- Use more powerful model (GPT-4.1) for better adaptation
+- Consider manual section annotation in LaTeX comments
+
+---
+
+### Scenario: Limited API Budget
+
+**Challenge**: Reducing costs while maintaining quality
+**Solution**:
+```bash
+# Use GPT-3.5-turbo for simple papers
+python pipeline_all.py \
+ --input-dir [paper_dir] \
+ --output-dir [output_dir] \
+ --model-choice 3
+
+# Generate only needed components
+# Website-only (cheapest)
+# Poster-only (moderate)
+# Video without talking-head (moderate)
+```
+
+---
+
+### Scenario: Tight Deadline
+
+**Challenge**: Need outputs quickly
+**Solution**:
+```bash
+# Parallel processing if multiple papers
+# Use faster models (GPT-3.5-turbo)
+# Generate only essential component first
+# Skip optional features (logo search, talking-head)
+
+python pipeline_light.py \
+ --model_name_t gpt-3.5-turbo \
+ --model_name_v gpt-3.5-turbo \
+ --result_dir [output_dir] \
+ --paper_latex_root [latex_dir]
+```
+
+**Priority Order**:
+1. Website (fastest, most versatile)
+2. Poster (moderate speed, print deadline)
+3. Video (slowest, can be generated later)
+
+---
+
+## Quality Optimization Tips
+
+### For Best Website Results
+1. Use LaTeX input with all assets
+2. Include high-resolution figures
+3. Ensure paper has clear section structure
+4. Enable logo search for professional appearance
+5. Review and test all interactive elements
+
+### For Best Poster Results
+1. Provide high-resolution figures (300+ DPI)
+2. Specify exact poster dimensions needed
+3. Include institution branding information
+4. Use professional color scheme
+5. Test print small preview before full poster
+
+### For Best Video Results
+1. Use LaTeX for clearest content extraction
+2. Specify target duration appropriately
+3. Review script before video generation
+4. Choose appropriate presentation style
+5. Test audio quality and pacing
+
+### For Best Overall Results
+1. Start with clean, well-organized LaTeX source
+2. Use GPT-4 or GPT-4.1 for highest quality
+3. Review all outputs before finalizing
+4. Iterate on any component that needs adjustment
+5. Combine components for cohesive presentation package
diff --git a/scientific-skills/peer-review/SKILL.md b/scientific-skills/peer-review/SKILL.md
new file mode 100644
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+---
+name: peer-review
+description: "Systematic peer review toolkit. Evaluate methodology, statistics, design, reproducibility, ethics, figure integrity, reporting standards, for manuscript and grant review across disciplines."
+allowed-tools: [Read, Write, Edit, Bash]
+---
+
+# Scientific Critical Evaluation and Peer Review
+
+## Overview
+
+Peer review is a systematic process for evaluating scientific manuscripts. Assess methodology, statistics, design, reproducibility, ethics, and reporting standards. Apply this skill for manuscript and grant review across disciplines with constructive, rigorous evaluation.
+
+## When to Use This Skill
+
+This skill should be used when:
+- Conducting peer review of scientific manuscripts for journals
+- Evaluating grant proposals and research applications
+- Assessing methodology and experimental design rigor
+- Reviewing statistical analyses and reporting standards
+- Evaluating reproducibility and data availability
+- Checking compliance with reporting guidelines (CONSORT, STROBE, PRISMA)
+- Providing constructive feedback on scientific writing
+
+## Visual Enhancement with Scientific Schematics
+
+**When creating documents with this skill, always consider adding scientific diagrams and schematics to enhance visual communication.**
+
+If your document does not already contain schematics or diagrams:
+- Use the **scientific-schematics** skill to generate AI-powered publication-quality diagrams
+- Simply describe your desired diagram in natural language
+- Nano Banana Pro will automatically generate, review, and refine the schematic
+
+**For new documents:** Scientific schematics should be generated by default to visually represent key concepts, workflows, architectures, or relationships described in the text.
+
+**How to generate schematics:**
+```bash
+python scripts/generate_schematic.py "your diagram description" -o figures/output.png
+```
+
+The AI will automatically:
+- Create publication-quality images with proper formatting
+- Review and refine through multiple iterations
+- Ensure accessibility (colorblind-friendly, high contrast)
+- Save outputs in the figures/ directory
+
+**When to add schematics:**
+- Peer review workflow diagrams
+- Evaluation criteria decision trees
+- Review process flowcharts
+- Methodology assessment frameworks
+- Quality assessment visualizations
+- Reporting guidelines compliance diagrams
+- Any complex concept that benefits from visualization
+
+For detailed guidance on creating schematics, refer to the scientific-schematics skill documentation.
+
+---
+
+## Peer Review Workflow
+
+Conduct peer review systematically through the following stages, adapting depth and focus based on the manuscript type and discipline.
+
+### Stage 1: Initial Assessment
+
+Begin with a high-level evaluation to determine the manuscript's scope, novelty, and overall quality.
+
+**Key Questions:**
+- What is the central research question or hypothesis?
+- What are the main findings and conclusions?
+- Is the work scientifically sound and significant?
+- Is the work appropriate for the intended venue?
+- Are there any immediate major flaws that would preclude publication?
+
+**Output:** Brief summary (2-3 sentences) capturing the manuscript's essence and initial impression.
+
+### Stage 2: Detailed Section-by-Section Review
+
+Conduct a thorough evaluation of each manuscript section, documenting specific concerns and strengths.
+
+#### Abstract and Title
+- **Accuracy:** Does the abstract accurately reflect the study's content and conclusions?
+- **Clarity:** Is the title specific, accurate, and informative?
+- **Completeness:** Are key findings and methods summarized appropriately?
+- **Accessibility:** Is the abstract comprehensible to a broad scientific audience?
+
+#### Introduction
+- **Context:** Is the background information adequate and current?
+- **Rationale:** Is the research question clearly motivated and justified?
+- **Novelty:** Is the work's originality and significance clearly articulated?
+- **Literature:** Are relevant prior studies appropriately cited?
+- **Objectives:** Are research aims/hypotheses clearly stated?
+
+#### Methods
+- **Reproducibility:** Can another researcher replicate the study from the description provided?
+- **Rigor:** Are the methods appropriate for addressing the research questions?
+- **Detail:** Are protocols, reagents, equipment, and parameters sufficiently described?
+- **Ethics:** Are ethical approvals, consent, and data handling properly documented?
+- **Statistics:** Are statistical methods appropriate, clearly described, and justified?
+- **Validation:** Are controls, replicates, and validation approaches adequate?
+
+**Critical elements to verify:**
+- Sample sizes and power calculations
+- Randomization and blinding procedures
+- Inclusion/exclusion criteria
+- Data collection protocols
+- Computational methods and software versions
+- Statistical tests and correction for multiple comparisons
+
+#### Results
+- **Presentation:** Are results presented logically and clearly?
+- **Figures/Tables:** Are visualizations appropriate, clear, and properly labeled?
+- **Statistics:** Are statistical results properly reported (effect sizes, confidence intervals, p-values)?
+- **Objectivity:** Are results presented without over-interpretation?
+- **Completeness:** Are all relevant results included, including negative results?
+- **Reproducibility:** Are raw data or summary statistics provided?
+
+**Common issues to identify:**
+- Selective reporting of results
+- Inappropriate statistical tests
+- Missing error bars or measures of variability
+- Over-fitting or circular analysis
+- Batch effects or confounding variables
+- Missing controls or validation experiments
+
+#### Discussion
+- **Interpretation:** Are conclusions supported by the data?
+- **Limitations:** Are study limitations acknowledged and discussed?
+- **Context:** Are findings placed appropriately within existing literature?
+- **Speculation:** Is speculation clearly distinguished from data-supported conclusions?
+- **Significance:** Are implications and importance clearly articulated?
+- **Future directions:** Are next steps or unanswered questions discussed?
+
+**Red flags:**
+- Overstated conclusions
+- Ignoring contradictory evidence
+- Causal claims from correlational data
+- Inadequate discussion of limitations
+- Mechanistic claims without mechanistic evidence
+
+#### References
+- **Completeness:** Are key relevant papers cited?
+- **Currency:** Are recent important studies included?
+- **Balance:** Are contrary viewpoints appropriately cited?
+- **Accuracy:** Are citations accurate and appropriate?
+- **Self-citation:** Is there excessive or inappropriate self-citation?
+
+### Stage 3: Methodological and Statistical Rigor
+
+Evaluate the technical quality and rigor of the research with particular attention to common pitfalls.
+
+**Statistical Assessment:**
+- Are statistical assumptions met (normality, independence, homoscedasticity)?
+- Are effect sizes reported alongside p-values?
+- Is multiple testing correction applied appropriately?
+- Are confidence intervals provided?
+- Is sample size justified with power analysis?
+- Are parametric vs. non-parametric tests chosen appropriately?
+- Are missing data handled properly?
+- Are exploratory vs. confirmatory analyses distinguished?
+
+**Experimental Design:**
+- Are controls appropriate and adequate?
+- Is replication sufficient (biological and technical)?
+- Are potential confounders identified and controlled?
+- Is randomization properly implemented?
+- Are blinding procedures adequate?
+- Is the experimental design optimal for the research question?
+
+**Computational/Bioinformatics:**
+- Are computational methods clearly described and justified?
+- Are software versions and parameters documented?
+- Is code made available for reproducibility?
+- Are algorithms and models validated appropriately?
+- Are assumptions of computational methods met?
+- Is batch correction applied appropriately?
+
+### Stage 4: Reproducibility and Transparency
+
+Assess whether the research meets modern standards for reproducibility and open science.
+
+**Data Availability:**
+- Are raw data deposited in appropriate repositories?
+- Are accession numbers provided for public databases?
+- Are data sharing restrictions justified (e.g., patient privacy)?
+- Are data formats standard and accessible?
+
+**Code and Materials:**
+- Is analysis code made available (GitHub, Zenodo, etc.)?
+- Are unique materials available or described sufficiently for recreation?
+- Are protocols detailed in sufficient depth?
+
+**Reporting Standards:**
+- Does the manuscript follow discipline-specific reporting guidelines (CONSORT, PRISMA, ARRIVE, MIAME, MINSEQE, etc.)?
+- See `references/reporting_standards.md` for common guidelines
+- Are all elements of the appropriate checklist addressed?
+
+### Stage 5: Figure and Data Presentation
+
+Evaluate the quality, clarity, and integrity of data visualization.
+
+**Quality Checks:**
+- Are figures high resolution and clearly labeled?
+- Are axes properly labeled with units?
+- Are error bars defined (SD, SEM, CI)?
+- Are statistical significance indicators explained?
+- Are color schemes appropriate and accessible (colorblind-friendly)?
+- Are scale bars included for images?
+- Is data visualization appropriate for the data type?
+
+**Integrity Checks:**
+- Are there signs of image manipulation (duplications, splicing)?
+- Are Western blots and gels appropriately presented?
+- Are representative images truly representative?
+- Are all conditions shown (no selective presentation)?
+
+**Clarity:**
+- Can figures stand alone with their legends?
+- Is the message of each figure immediately clear?
+- Are there redundant figures or panels?
+- Would data be better presented as tables or figures?
+
+### Stage 6: Ethical Considerations
+
+Verify that the research meets ethical standards and guidelines.
+
+**Human Subjects:**
+- Is IRB/ethics approval documented?
+- Is informed consent described?
+- Are vulnerable populations appropriately protected?
+- Is patient privacy adequately protected?
+- Are potential conflicts of interest disclosed?
+
+**Animal Research:**
+- Is IACUC or equivalent approval documented?
+- Are procedures humane and justified?
+- Are the 3Rs (replacement, reduction, refinement) considered?
+- Are euthanasia methods appropriate?
+
+**Research Integrity:**
+- Are there concerns about data fabrication or falsification?
+- Is authorship appropriate and justified?
+- Are competing interests disclosed?
+- Is funding source disclosed?
+- Are there concerns about plagiarism or duplicate publication?
+
+### Stage 7: Writing Quality and Clarity
+
+Assess the manuscript's clarity, organization, and accessibility.
+
+**Structure and Organization:**
+- Is the manuscript logically organized?
+- Do sections flow coherently?
+- Are transitions between ideas clear?
+- Is the narrative compelling and clear?
+
+**Writing Quality:**
+- Is the language clear, precise, and concise?
+- Are jargon and acronyms minimized and defined?
+- Is grammar and spelling correct?
+- Are sentences unnecessarily complex?
+- Is the passive voice overused?
+
+**Accessibility:**
+- Can a non-specialist understand the main findings?
+- Are technical terms explained?
+- Is the significance clear to a broad audience?
+
+## Structuring Peer Review Reports
+
+Organize feedback in a hierarchical structure that prioritizes issues and provides actionable guidance.
+
+### Summary Statement
+
+Provide a concise overall assessment (1-2 paragraphs):
+- Brief synopsis of the research
+- Overall recommendation (accept, minor revisions, major revisions, reject)
+- Key strengths (2-3 bullet points)
+- Key weaknesses (2-3 bullet points)
+- Bottom-line assessment of significance and soundness
+
+### Major Comments
+
+List critical issues that significantly impact the manuscript's validity, interpretability, or significance. Number these sequentially for easy reference.
+
+**Major comments typically include:**
+- Fundamental methodological flaws
+- Inappropriate statistical analyses
+- Unsupported or overstated conclusions
+- Missing critical controls or experiments
+- Serious reproducibility concerns
+- Major gaps in literature coverage
+- Ethical concerns
+
+**For each major comment:**
+1. Clearly state the issue
+2. Explain why it's problematic
+3. Suggest specific solutions or additional experiments
+4. Indicate if addressing it is essential for publication
+
+### Minor Comments
+
+List less critical issues that would improve clarity, completeness, or presentation. Number these sequentially.
+
+**Minor comments typically include:**
+- Unclear figure labels or legends
+- Missing methodological details
+- Typographical or grammatical errors
+- Suggestions for improved data presentation
+- Minor statistical reporting issues
+- Supplementary analyses that would strengthen conclusions
+- Requests for clarification
+
+**For each minor comment:**
+1. Identify the specific location (section, paragraph, figure)
+2. State the issue clearly
+3. Suggest how to address it
+
+### Specific Line-by-Line Comments (Optional)
+
+For manuscripts requiring detailed feedback, provide section-specific or line-by-line comments:
+- Reference specific page/line numbers or sections
+- Note factual errors, unclear statements, or missing citations
+- Suggest specific edits for clarity
+
+### Questions for Authors
+
+List specific questions that need clarification:
+- Methodological details that are unclear
+- Seemingly contradictory results
+- Missing information needed to evaluate the work
+- Requests for additional data or analyses
+
+## Tone and Approach
+
+Maintain a constructive, professional, and collegial tone throughout the review.
+
+**Best Practices:**
+- **Be constructive:** Frame criticism as opportunities for improvement
+- **Be specific:** Provide concrete examples and actionable suggestions
+- **Be balanced:** Acknowledge strengths as well as weaknesses
+- **Be respectful:** Remember that authors have invested significant effort
+- **Be objective:** Focus on the science, not the scientists
+- **Be thorough:** Don't overlook issues, but prioritize appropriately
+- **Be clear:** Avoid ambiguous or vague criticism
+
+**Avoid:**
+- Personal attacks or dismissive language
+- Sarcasm or condescension
+- Vague criticism without specific examples
+- Requesting unnecessary experiments beyond the scope
+- Demanding adherence to personal preferences vs. best practices
+- Revealing your identity if reviewing is double-blind
+
+## Special Considerations by Manuscript Type
+
+### Original Research Articles
+- Emphasize rigor, reproducibility, and novelty
+- Assess significance and impact
+- Verify that conclusions are data-driven
+- Check for complete methods and appropriate controls
+
+### Reviews and Meta-Analyses
+- Evaluate comprehensiveness of literature coverage
+- Assess search strategy and inclusion/exclusion criteria
+- Verify systematic approach and lack of bias
+- Check for critical analysis vs. mere summarization
+- For meta-analyses, evaluate statistical approach and heterogeneity
+
+### Methods Papers
+- Emphasize validation and comparison to existing methods
+- Assess reproducibility and availability of protocols/code
+- Evaluate improvements over existing approaches
+- Check for sufficient detail for implementation
+
+### Short Reports/Letters
+- Adapt expectations for brevity
+- Ensure core findings are still rigorous and significant
+- Verify that format is appropriate for findings
+
+### Preprints
+- Recognize that these have not undergone formal peer review
+- May be less polished than journal submissions
+- Still apply rigorous standards for scientific validity
+- Consider providing constructive feedback to help authors improve before journal submission
+
+### Presentations and Slide Decks
+
+**⚠️ CRITICAL: For presentations, NEVER read the PDF directly. ALWAYS convert to images first.**
+
+When reviewing scientific presentations (PowerPoint, Beamer, slide decks):
+
+#### Mandatory Image-Based Review Workflow
+
+**NEVER attempt to read presentation PDFs directly** - this causes buffer overflow errors and doesn't show visual formatting issues.
+
+**Required Process:**
+1. Convert PDF to images using Python:
+ ```bash
+ python skills/scientific-slides/scripts/pdf_to_images.py presentation.pdf review/slide --dpi 150
+ # Creates: review/slide-001.jpg, review/slide-002.jpg, etc.
+ ```
+2. Read and inspect EACH slide image file sequentially
+3. Document issues with specific slide numbers
+4. Provide feedback on visual formatting and content
+
+**Print when starting review:**
+```
+[HH:MM:SS] PEER REVIEW: Presentation detected - converting to images for review
+[HH:MM:SS] PDF REVIEW: NEVER reading PDF directly - using image-based inspection
+```
+
+#### Presentation-Specific Evaluation Criteria
+
+**Visual Design and Readability:**
+- [ ] Text is large enough (minimum 18pt, ideally 24pt+ for body text)
+- [ ] High contrast between text and background (4.5:1 minimum, 7:1 preferred)
+- [ ] Color scheme is professional and colorblind-accessible
+- [ ] Consistent visual design across all slides
+- [ ] White space is adequate (not cramped)
+- [ ] Fonts are clear and professional
+
+**Layout and Formatting (Check EVERY Slide Image):**
+- [ ] No text overflow or truncation at slide edges
+- [ ] No element overlaps (text over images, overlapping shapes)
+- [ ] Titles are consistently positioned
+- [ ] Content is properly aligned
+- [ ] Bullets and text are not cut off
+- [ ] Figures fit within slide boundaries
+- [ ] Captions and labels are visible and readable
+
+**Content Quality:**
+- [ ] One main idea per slide (not overloaded)
+- [ ] Minimal text (3-6 bullets per slide maximum)
+- [ ] Bullet points are concise (5-7 words each)
+- [ ] Figures are simplified and clear (not copy-pasted from papers)
+- [ ] Data visualizations have large, readable labels
+- [ ] Citations are present and properly formatted
+- [ ] Results/data slides dominate the presentation (40-50% of content)
+
+**Structure and Flow:**
+- [ ] Clear narrative arc (introduction → methods → results → discussion)
+- [ ] Logical progression between slides
+- [ ] Slide count appropriate for talk duration (~1 slide per minute)
+- [ ] Title slide includes authors, affiliation, date
+- [ ] Introduction cites relevant background literature (3-5 papers)
+- [ ] Discussion cites comparison papers (3-5 papers)
+- [ ] Conclusions slide summarizes key findings
+- [ ] Acknowledgments/funding slide at end
+
+**Scientific Content:**
+- [ ] Research question clearly stated
+- [ ] Methods adequately summarized (not excessive detail)
+- [ ] Results presented logically with clear visualizations
+- [ ] Statistical significance indicated appropriately
+- [ ] Conclusions supported by data shown
+- [ ] Limitations acknowledged where appropriate
+- [ ] Future directions or broader impact discussed
+
+**Common Presentation Issues to Flag:**
+
+**Critical Issues (Must Fix):**
+- Text overflow making content unreadable
+- Font sizes too small (<18pt)
+- Element overlaps obscuring data
+- Insufficient contrast (text hard to read)
+- Figures too complex or illegible
+- No citations (completely unsupported claims)
+- Slide count drastically mismatched to duration
+
+**Major Issues (Should Fix):**
+- Inconsistent design across slides
+- Too much text (walls of text, not bullets)
+- Poorly simplified figures (axis labels too small)
+- Cramped layout with insufficient white space
+- Missing key structural elements (no conclusion slide)
+- Poor color choices (not colorblind-safe)
+- Minimal results content (<30% of slides)
+
+**Minor Issues (Suggestions for Improvement):**
+- Could use more visuals/diagrams
+- Some slides slightly text-heavy
+- Minor alignment inconsistencies
+- Could benefit from more white space
+- Additional citations would strengthen claims
+- Color scheme could be more modern
+
+#### Review Report Format for Presentations
+
+**Summary Statement:**
+- Overall impression of presentation quality
+- Appropriateness for target audience and duration
+- Key strengths (visual design, content, clarity)
+- Key weaknesses (formatting issues, content gaps)
+- Recommendation (ready to present, minor revisions, major revisions)
+
+**Layout and Formatting Issues (By Slide Number):**
+```
+Slide 3: Text overflow - bullet point 4 extends beyond right margin
+Slide 7: Element overlap - figure overlaps with caption text
+Slide 12: Font size - axis labels too small to read from distance
+Slide 18: Alignment - title not centered
+```
+
+**Content and Structure Feedback:**
+- Adequacy of background context and citations
+- Clarity of research question and objectives
+- Quality of methods summary
+- Effectiveness of results presentation
+- Strength of conclusions and implications
+
+**Design and Accessibility:**
+- Overall visual appeal and professionalism
+- Color contrast and readability
+- Colorblind accessibility
+- Consistency across slides
+
+**Timing and Scope:**
+- Whether slide count matches intended duration
+- Appropriate level of detail for talk type
+- Balance between sections
+
+#### Example Image-Based Review Process
+
+```
+[14:30:00] PEER REVIEW: Starting review of presentation
+[14:30:05] PEER REVIEW: Presentation detected - converting to images
+[14:30:10] PDF REVIEW: Running pdf_to_images.py on presentation.pdf
+[14:30:15] PDF REVIEW: Converted 25 slides to images in review/ directory
+[14:30:20] PDF REVIEW: Inspecting slide 1/25 - title slide
+[14:30:25] PDF REVIEW: Inspecting slide 2/25 - introduction
+...
+[14:35:40] PDF REVIEW: Inspecting slide 25/25 - acknowledgments
+[14:35:45] PDF REVIEW: Completed image-based review
+[14:35:50] PEER REVIEW: Found 8 layout issues, 3 content issues
+[14:35:55] PEER REVIEW: Generating structured feedback by slide number
+```
+
+**Remember:** For presentations, the visual inspection via images is MANDATORY. Never attempt to read presentation PDFs as text - it will fail and miss all visual formatting issues.
+
+## Resources
+
+This skill includes reference materials to support comprehensive peer review:
+
+### references/reporting_standards.md
+Guidelines for major reporting standards across disciplines (CONSORT, PRISMA, ARRIVE, MIAME, STROBE, etc.) to evaluate completeness of methods and results reporting.
+
+### references/common_issues.md
+Catalog of frequent methodological and statistical issues encountered in peer review, with guidance on identifying and addressing them.
+
+## Final Checklist
+
+Before finalizing the review, verify:
+
+- [ ] Summary statement clearly conveys overall assessment
+- [ ] Major concerns are clearly identified and justified
+- [ ] Suggested revisions are specific and actionable
+- [ ] Minor issues are noted but properly categorized
+- [ ] Statistical methods have been evaluated
+- [ ] Reproducibility and data availability assessed
+- [ ] Ethical considerations verified
+- [ ] Figures and tables evaluated for quality and integrity
+- [ ] Writing quality assessed
+- [ ] Tone is constructive and professional throughout
+- [ ] Review is thorough but proportionate to manuscript scope
+- [ ] Recommendation is consistent with identified issues
diff --git a/scientific-skills/peer-review/references/common_issues.md b/scientific-skills/peer-review/references/common_issues.md
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+# Common Methodological and Statistical Issues in Scientific Manuscripts
+
+This document catalogs frequent issues encountered during peer review, organized by category. Use this as a reference to identify potential problems and provide constructive feedback.
+
+## Statistical Issues
+
+### 1. P-Value Misuse and Misinterpretation
+
+**Common Problems:**
+- P-hacking (selective reporting of significant results)
+- Multiple testing without correction (familywise error rate inflation)
+- Interpreting non-significance as proof of no effect
+- Focusing exclusively on p-values without effect sizes
+- Dichotomizing continuous p-values at arbitrary thresholds (p=0.049 vs p=0.051)
+- Confusing statistical significance with biological/clinical significance
+
+**How to Identify:**
+- Suspiciously high proportion of p-values just below 0.05
+- Many tests performed but no correction mentioned
+- Statements like "no difference was found" from non-significant results
+- No effect sizes or confidence intervals reported
+- Language suggesting p-values indicate strength of effect
+
+**What to Recommend:**
+- Report effect sizes with confidence intervals
+- Apply appropriate multiple testing corrections (Bonferroni, FDR, Holm-Bonferroni)
+- Interpret non-significance cautiously (lack of evidence ≠ evidence of lack)
+- Pre-register analyses to avoid p-hacking
+- Consider equivalence testing for "no difference" claims
+
+### 2. Inappropriate Statistical Tests
+
+**Common Problems:**
+- Using parametric tests when assumptions are violated (non-normal data, unequal variances)
+- Analyzing paired data with unpaired tests
+- Using t-tests for multiple groups instead of ANOVA with post-hoc tests
+- Treating ordinal data as continuous
+- Ignoring repeated measures structure
+- Using correlation when regression is more appropriate
+
+**How to Identify:**
+- No mention of assumption checking
+- Small sample sizes with parametric tests
+- Multiple pairwise t-tests instead of ANOVA
+- Likert scales analyzed with t-tests
+- Time-series data analyzed without accounting for repeated measures
+
+**What to Recommend:**
+- Check assumptions explicitly (normality tests, Q-Q plots)
+- Use non-parametric alternatives when appropriate
+- Apply proper corrections for multiple comparisons after ANOVA
+- Use mixed-effects models for repeated measures
+- Consider ordinal regression for ordinal outcomes
+
+### 3. Sample Size and Power Issues
+
+**Common Problems:**
+- No sample size justification or power calculation
+- Underpowered studies claiming "no effect"
+- Post-hoc power calculations (which are uninformative)
+- Stopping rules not pre-specified
+- Unequal group sizes without justification
+
+**How to Identify:**
+- Small sample sizes (n<30 per group for typical designs)
+- No mention of power analysis in methods
+- Statements about post-hoc power
+- Wide confidence intervals suggesting imprecision
+- Claims of "no effect" with large p-values and small n
+
+**What to Recommend:**
+- Conduct a priori power analysis based on expected effect size
+- Report achieved power or precision (confidence interval width)
+- Acknowledge when studies are underpowered
+- Consider effect sizes and confidence intervals for interpretation
+- Pre-register sample size and stopping rules
+
+### 4. Missing Data Problems
+
+**Common Problems:**
+- Complete case analysis without justification (listwise deletion)
+- Not reporting extent or pattern of missingness
+- Assuming data are missing completely at random (MCAR) without testing
+- Inappropriate imputation methods
+- Not performing sensitivity analyses
+
+**How to Identify:**
+- Different n values across analyses without explanation
+- No discussion of missing data
+- Participants "excluded from analysis"
+- Simple mean imputation used
+- No sensitivity analyses comparing complete vs. imputed data
+
+**What to Recommend:**
+- Report extent and patterns of missingness
+- Test MCAR assumption (Little's test)
+- Use appropriate methods (multiple imputation, maximum likelihood)
+- Perform sensitivity analyses
+- Consider intention-to-treat analysis for trials
+
+### 5. Circular Analysis and Double-Dipping
+
+**Common Problems:**
+- Using the same data for selection and inference
+- Defining ROIs based on contrast then testing that contrast in same ROI
+- Selecting outliers then testing for differences
+- Post-hoc subgroup analyses presented as planned
+- HARKing (Hypothesizing After Results are Known)
+
+**How to Identify:**
+- ROIs or features selected based on results
+- Unexpected subgroup analyses
+- Post-hoc analyses not clearly labeled as exploratory
+- No data-independent validation
+- Introduction that perfectly predicts findings
+
+**What to Recommend:**
+- Use independent datasets for selection and testing
+- Pre-register analyses and hypotheses
+- Clearly distinguish confirmatory vs. exploratory analyses
+- Use cross-validation or hold-out datasets
+- Correct for selection bias
+
+### 6. Pseudoreplication
+
+**Common Problems:**
+- Technical replicates treated as biological replicates
+- Multiple measurements from same subject treated as independent
+- Clustered data analyzed without accounting for clustering
+- Non-independence in spatial or temporal data
+
+**How to Identify:**
+- n defined as number of measurements rather than biological units
+- Multiple cells from same animal counted as independent
+- Repeated measures not acknowledged
+- No mention of random effects or clustering
+
+**What to Recommend:**
+- Define n as biological replicates (animals, patients, independent samples)
+- Use mixed-effects models for nested or clustered data
+- Account for repeated measures explicitly
+- Average technical replicates before analysis
+- Report both technical and biological replication
+
+## Experimental Design Issues
+
+### 7. Lack of Appropriate Controls
+
+**Common Problems:**
+- Missing negative controls
+- Missing positive controls for validation
+- No vehicle controls for drug studies
+- No time-matched controls for longitudinal studies
+- No batch controls
+
+**How to Identify:**
+- Methods section lists only experimental groups
+- No mention of controls in figures
+- Unclear baseline or reference condition
+- Cross-batch comparisons without controls
+
+**What to Recommend:**
+- Include negative controls to assess specificity
+- Include positive controls to validate methods
+- Use vehicle controls matched to experimental treatment
+- Include sham surgery controls for surgical interventions
+- Include batch controls for cross-batch comparisons
+
+### 8. Confounding Variables
+
+**Common Problems:**
+- Systematic differences between groups besides intervention
+- Batch effects not controlled or corrected
+- Order effects in sequential experiments
+- Time-of-day effects not controlled
+- Experimenter effects not blinded
+
+**How to Identify:**
+- Groups differ in multiple characteristics
+- Samples processed in different batches by group
+- No randomization of sample order
+- No mention of blinding
+- Baseline characteristics differ between groups
+
+**What to Recommend:**
+- Randomize experimental units to conditions
+- Block on known confounders
+- Randomize sample processing order
+- Use blinding to minimize bias
+- Perform batch correction if needed
+- Report and adjust for baseline differences
+
+### 9. Insufficient Replication
+
+**Common Problems:**
+- Single experiment without replication
+- Technical replicates mistaken for biological replication
+- Small n justified by "typical for the field"
+- No independent validation of key findings
+- Cherry-picking representative examples
+
+**How to Identify:**
+- Methods state "experiment performed once"
+- n=3 with no justification
+- "Representative image shown"
+- Key claims based on single experiment
+- No validation in independent dataset
+
+**What to Recommend:**
+- Perform independent biological replicates (typically ≥3)
+- Validate key findings in independent cohorts
+- Report all replicates, not just representative examples
+- Conduct power analysis to justify sample size
+- Show individual data points, not just summary statistics
+
+## Reproducibility Issues
+
+### 10. Insufficient Methodological Detail
+
+**Common Problems:**
+- Methods not described in sufficient detail for replication
+- Key reagents not specified (vendor, catalog number)
+- Software versions and parameters not reported
+- Antibodies not validated
+- Cell line authentication not verified
+
+**How to Identify:**
+- Vague descriptions ("standard protocols were used")
+- No information on reagent sources
+- Generic software mentioned without versions
+- No antibody validation information
+- Cell lines not authenticated
+
+**What to Recommend:**
+- Provide detailed protocols or cite specific protocols
+- Include reagent vendors, catalog numbers, lot numbers
+- Report software versions and all parameters
+- Include antibody validation (Western blot, specificity tests)
+- Report cell line authentication method (STR profiling)
+- Make protocols available (protocols.io, supplementary materials)
+
+### 11. Data and Code Availability
+
+**Common Problems:**
+- No data availability statement
+- "Data available upon request" (often unfulfilled)
+- No code provided for computational analyses
+- Custom software not made available
+- No clear documentation
+
+**How to Identify:**
+- Missing data availability statement
+- No repository accession numbers
+- Computational methods with no code
+- Custom pipelines without access
+- No README or documentation
+
+**What to Recommend:**
+- Deposit raw data in appropriate repositories (GEO, SRA, Dryad, Zenodo)
+- Share analysis code on GitHub or similar
+- Provide clear documentation and README files
+- Include requirements.txt or environment files
+- Make custom software available with installation instructions
+- Use DOIs for permanent data citation
+
+### 12. Lack of Method Validation
+
+**Common Problems:**
+- New methods not compared to gold standard
+- Assays not validated for specificity, sensitivity, linearity
+- No spike-in controls
+- Cross-reactivity not tested
+- Detection limits not established
+
+**How to Identify:**
+- Novel assays presented without validation
+- No comparison to existing methods
+- No positive/negative controls shown
+- Claims of specificity without evidence
+- No standard curves or controls
+
+**What to Recommend:**
+- Validate new methods against established approaches
+- Show specificity (knockdown/knockout controls)
+- Demonstrate linearity and dynamic range
+- Include positive and negative controls
+- Report limits of detection and quantification
+- Show reproducibility across replicates and operators
+
+## Interpretation Issues
+
+### 13. Overstatement of Results
+
+**Common Problems:**
+- Causal language for correlational data
+- Mechanistic claims without mechanistic evidence
+- Extrapolating beyond data (species, conditions, populations)
+- Claiming "first to show" without thorough literature review
+- Overgeneralizing from limited samples
+
+**How to Identify:**
+- "X causes Y" from observational data
+- Mechanism proposed without direct testing
+- Mouse data presented as relevant to humans without caveats
+- Claims of novelty with missing citations
+- Broad claims from narrow samples
+
+**What to Recommend:**
+- Use appropriate language ("associated with" vs. "caused by")
+- Distinguish correlation from causation
+- Acknowledge limitations of model systems
+- Provide thorough literature context
+- Be specific about generalizability
+- Propose mechanisms as hypotheses, not conclusions
+
+### 14. Cherry-Picking and Selective Reporting
+
+**Common Problems:**
+- Reporting only significant results
+- Showing "representative" images that may not be typical
+- Excluding outliers without justification
+- Not reporting negative or contradictory findings
+- Switching between different statistical approaches
+
+**How to Identify:**
+- All reported results are significant
+- "Representative of 3 experiments" with no quantification
+- Data exclusions mentioned in results but not methods
+- Supplementary data contradicts main findings
+- Multiple analysis approaches with only one reported
+
+**What to Recommend:**
+- Report all planned analyses regardless of outcome
+- Quantify and show variability across replicates
+- Pre-specify outlier exclusion criteria
+- Include negative results
+- Pre-register analysis plan
+- Report effect sizes and confidence intervals for all comparisons
+
+### 15. Ignoring Alternative Explanations
+
+**Common Problems:**
+- Preferred explanation presented without considering alternatives
+- Contradictory evidence dismissed without discussion
+- Off-target effects not considered
+- Confounding variables not acknowledged
+- Limitations section minimal or absent
+
+**How to Identify:**
+- Single interpretation presented as fact
+- Prior contradictory findings not cited or discussed
+- No consideration of alternative mechanisms
+- No discussion of limitations
+- Specificity assumed without controls
+
+**What to Recommend:**
+- Discuss alternative explanations
+- Address contradictory findings from literature
+- Include appropriate specificity controls
+- Acknowledge and discuss limitations thoroughly
+- Consider and test alternative hypotheses
+
+## Figure and Data Presentation Issues
+
+### 16. Inappropriate Data Visualization
+
+**Common Problems:**
+- Bar graphs for continuous data (hiding distributions)
+- No error bars or error bars not defined
+- Truncated y-axes exaggerating differences
+- Dual y-axes creating misleading comparisons
+- Too many significant figures
+- Colors not colorblind-friendly
+
+**How to Identify:**
+- Bar graphs with few data points
+- Unclear what error bars represent (SD, SEM, CI?)
+- Y-axis doesn't start at zero for ratio/percentage data
+- Left and right y-axes with different scales
+- Values reported to excessive precision (p=0.04562)
+- Red-green color schemes
+
+**What to Recommend:**
+- Show individual data points with scatter/box/violin plots
+- Always define error bars (SD, SEM, 95% CI)
+- Start y-axis at zero or indicate breaks clearly
+- Avoid dual y-axes; use separate panels instead
+- Report appropriate significant figures
+- Use colorblind-friendly palettes (viridis, colorbrewer)
+- Include sample sizes in figure legends
+
+### 17. Image Manipulation Concerns
+
+**Common Problems:**
+- Excessive contrast/brightness adjustment
+- Spliced gels or images without indication
+- Duplicated images or panels
+- Uneven background in Western blots
+- Selective cropping
+- Over-processed microscopy images
+
+**How to Identify:**
+- Suspicious patterns or discontinuities
+- Very high contrast with no background
+- Similar features in different panels
+- Straight lines suggesting splicing
+- Inconsistent backgrounds
+- Loss of detail suggesting over-processing
+
+**What to Recommend:**
+- Apply adjustments uniformly across images
+- Indicate spliced gels with dividing lines
+- Show full, uncropped images in supplementary materials
+- Provide original images if requested
+- Follow journal image integrity policies
+- Use appropriate image analysis tools
+
+## Study Design Issues
+
+### 18. Poorly Defined Hypotheses and Outcomes
+
+**Common Problems:**
+- No clear hypothesis stated
+- Primary outcome not specified
+- Multiple outcomes without correction
+- Outcomes changed after data collection
+- Fishing expeditions presented as hypothesis-driven
+
+**How to Identify:**
+- Introduction doesn't state clear testable hypothesis
+- Multiple outcomes with unclear hierarchy
+- Outcomes in results don't match those in methods
+- Exploratory study presented as confirmatory
+- Many tests with no multiple testing correction
+
+**What to Recommend:**
+- State clear, testable hypotheses
+- Designate primary and secondary outcomes a priori
+- Pre-register studies when possible
+- Apply appropriate corrections for multiple outcomes
+- Clearly distinguish exploratory from confirmatory analyses
+- Report all pre-specified outcomes
+
+### 19. Baseline Imbalance and Selection Bias
+
+**Common Problems:**
+- Groups differ at baseline
+- Selection criteria applied differentially
+- Healthy volunteer bias
+- Survivorship bias
+- Indication bias in observational studies
+
+**How to Identify:**
+- Table 1 shows significant baseline differences
+- Inclusion criteria different between groups
+- Response rate <50% with no analysis
+- Analysis only includes completers
+- Groups self-selected rather than randomized
+
+**What to Recommend:**
+- Report baseline characteristics in Table 1
+- Use randomization to ensure balance
+- Adjust for baseline differences in analysis
+- Report response rates and compare responders vs. non-responders
+- Consider propensity score matching for observational data
+- Use intention-to-treat analysis
+
+### 20. Temporal and Batch Effects
+
+**Common Problems:**
+- Samples processed in batches by condition
+- Temporal trends not accounted for
+- Instrument drift over time
+- Different operators for different groups
+- Reagent lot changes between groups
+
+**How to Identify:**
+- All treatment samples processed on same day
+- Controls from different time period
+- No mention of batch or time effects
+- Different technicians for groups
+- Long study duration with no temporal analysis
+
+**What to Recommend:**
+- Randomize samples across batches/time
+- Include batch as covariate in analysis
+- Perform batch correction (ComBat, limma)
+- Include quality control samples across batches
+- Report and test for temporal trends
+- Balance operators across conditions
+
+## Reporting Issues
+
+### 21. Incomplete Statistical Reporting
+
+**Common Problems:**
+- Test statistics not reported
+- Degrees of freedom missing
+- Exact p-values replaced with inequalities (p<0.05)
+- No confidence intervals
+- No effect sizes
+- Sample sizes not reported per group
+
+**How to Identify:**
+- Only p-values given with no test statistics
+- p-values reported as p<0.05 rather than exact values
+- No measures of uncertainty
+- Effect magnitude unclear
+- n reported for total but not per group
+
+**What to Recommend:**
+- Report complete test statistics (t, F, χ², etc. with df)
+- Report exact p-values (except p<0.001)
+- Include 95% confidence intervals
+- Report effect sizes (Cohen's d, odds ratios, correlation coefficients)
+- Report n for each group in every analysis
+- Consider CONSORT-style flow diagram
+
+### 22. Methods-Results Mismatch
+
+**Common Problems:**
+- Methods describe analyses not performed
+- Results include analyses not described in methods
+- Different sample sizes in methods vs. results
+- Methods mention controls not shown
+- Statistical methods don't match what was done
+
+**How to Identify:**
+- Analyses in results without methodological description
+- Methods describe experiments not in results
+- Numbers don't match between sections
+- Controls mentioned but not shown
+- Different software mentioned than used
+
+**What to Recommend:**
+- Ensure complete concordance between methods and results
+- Describe all analyses performed in methods
+- Remove methodological descriptions of experiments not performed
+- Verify all numbers are consistent
+- Update methods to match actual analyses conducted
+
+## How to Use This Reference
+
+When reviewing manuscripts:
+1. Read through methods and results systematically
+2. Check for common issues in each category
+3. Note specific problems with evidence
+4. Provide constructive suggestions for improvement
+5. Distinguish major issues (affect validity) from minor issues (affect clarity)
+6. Prioritize reproducibility and transparency
+
+This is not an exhaustive list but covers the most frequently encountered issues. Always consider the specific context and discipline when evaluating potential problems.
diff --git a/scientific-skills/peer-review/references/reporting_standards.md b/scientific-skills/peer-review/references/reporting_standards.md
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+# Scientific Reporting Standards and Guidelines
+
+This document catalogs major reporting standards and guidelines across scientific disciplines. When reviewing manuscripts, verify that authors have followed the appropriate guidelines for their study type and discipline.
+
+## Clinical Trials and Medical Research
+
+### CONSORT (Consolidated Standards of Reporting Trials)
+**Purpose:** Randomized controlled trials (RCTs)
+**Key Requirements:**
+- Trial design, participants, and interventions clearly described
+- Primary and secondary outcomes specified
+- Sample size calculation and statistical methods
+- Participant flow through trial (enrollment, allocation, follow-up, analysis)
+- Baseline characteristics of participants
+- Numbers analyzed in each group
+- Outcomes and estimation with confidence intervals
+- Adverse events
+- Trial registration number and protocol access
+
+**Reference:** http://www.consort-statement.org/
+
+### STROBE (Strengthening the Reporting of Observational Studies in Epidemiology)
+**Purpose:** Observational studies (cohort, case-control, cross-sectional)
+**Key Requirements:**
+- Study design clearly stated
+- Setting, eligibility criteria, and participant sources
+- Variables clearly defined
+- Data sources and measurement methods
+- Bias assessment
+- Sample size justification
+- Statistical methods including handling of missing data
+- Participant flow and characteristics
+- Main results with confidence intervals
+- Limitations discussed
+
+**Reference:** https://www.strobe-statement.org/
+
+### PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses)
+**Purpose:** Systematic reviews and meta-analyses
+**Key Requirements:**
+- Protocol registration
+- Systematic search strategy across multiple databases
+- Inclusion/exclusion criteria
+- Study selection process
+- Data extraction methods
+- Quality assessment of included studies
+- Statistical methods for meta-analysis
+- Assessment of publication bias
+- Heterogeneity assessment
+- PRISMA flow diagram showing study selection
+- Summary of findings tables
+
+**Reference:** http://www.prisma-statement.org/
+
+### SPIRIT (Standard Protocol Items: Recommendations for Interventional Trials)
+**Purpose:** Clinical trial protocols
+**Key Requirements:**
+- Administrative information (title, registration, funding)
+- Introduction (rationale, objectives)
+- Methods (design, participants, interventions, outcomes, sample size)
+- Ethics and dissemination
+- Trial schedule and assessments
+
+**Reference:** https://www.spirit-statement.org/
+
+### CARE (CAse REport guidelines)
+**Purpose:** Case reports
+**Key Requirements:**
+- Patient information and demographics
+- Clinical findings
+- Timeline of events
+- Diagnostic assessment
+- Therapeutic interventions
+- Follow-up and outcomes
+- Patient perspective
+- Informed consent
+
+**Reference:** https://www.care-statement.org/
+
+## Animal Research
+
+### ARRIVE (Animal Research: Reporting of In Vivo Experiments)
+**Purpose:** Studies involving animal research
+**Key Requirements:**
+- Title indicates study involves animals
+- Abstract provides accurate summary
+- Background and objectives clearly stated
+- Ethical statement and approval
+- Housing and husbandry details
+- Animal details (species, strain, sex, age, weight)
+- Experimental procedures in detail
+- Experimental animals (number, allocation, welfare assessment)
+- Statistical methods appropriate
+- Exclusion criteria stated
+- Sample size determination
+- Randomization and blinding described
+- Outcome measures defined
+- Adverse events reported
+
+**Reference:** https://arriveguidelines.org/
+
+## Genomics and Molecular Biology
+
+### MIAME (Minimum Information About a Microarray Experiment)
+**Purpose:** Microarray experiments
+**Key Requirements:**
+- Experimental design clearly described
+- Array design information
+- Samples (origin, preparation, labeling)
+- Hybridization procedures and parameters
+- Image acquisition and quantification
+- Normalization and data transformation
+- Raw and processed data availability
+- Database accession numbers
+
+**Reference:** http://fged.org/projects/miame/
+
+### MINSEQE (Minimum Information about a high-throughput Nucleotide Sequencing Experiment)
+**Purpose:** High-throughput sequencing (RNA-seq, ChIP-seq, etc.)
+**Key Requirements:**
+- Experimental design and biological context
+- Sample information (source, preparation, QC)
+- Library preparation (protocol, adapters, size selection)
+- Sequencing platform and parameters
+- Data processing pipeline (alignment, quantification, normalization)
+- Quality control metrics
+- Raw data deposition (SRA, GEO, ENA)
+- Processed data and analysis code availability
+
+### MIGS/MIMS (Minimum Information about a Genome/Metagenome Sequence)
+**Purpose:** Genome and metagenome sequencing
+**Key Requirements:**
+- Sample origin and environmental context
+- Sequencing methods and coverage
+- Assembly methods and quality metrics
+- Annotation approach
+- Quality control and contamination screening
+- Data deposition in INSDC databases
+
+**Reference:** https://gensc.org/
+
+## Structural Biology
+
+### PDB (Protein Data Bank) Deposition Requirements
+**Purpose:** Macromolecular structure determination
+**Key Requirements:**
+- Atomic coordinates deposited
+- Structure factors for X-ray structures
+- Restraints and experimental data for NMR
+- EM maps and metadata for cryo-EM
+- Model quality validation metrics
+- Experimental conditions (crystallization, sample preparation)
+- Data collection parameters
+- Refinement statistics
+
+**Reference:** https://www.wwpdb.org/
+
+## Proteomics and Mass Spectrometry
+
+### MIAPE (Minimum Information About a Proteomics Experiment)
+**Purpose:** Proteomics experiments
+**Key Requirements:**
+- Sample processing and fractionation
+- Separation methods (2D gel, LC)
+- Mass spectrometry parameters (instrument, acquisition)
+- Database search and validation parameters
+- Peptide and protein identification criteria
+- Quantification methods
+- Statistical analysis
+- Data deposition (PRIDE, PeptideAtlas)
+
+**Reference:** http://www.psidev.info/
+
+## Neuroscience
+
+### COBIDAS (Committee on Best Practices in Data Analysis and Sharing)
+**Purpose:** MRI and fMRI studies
+**Key Requirements:**
+- Scanner and sequence parameters
+- Preprocessing pipeline details
+- Software versions and parameters
+- Statistical analysis approach
+- Multiple comparison correction
+- ROI definitions
+- Data sharing (raw data, analysis scripts)
+
+**Reference:** https://www.humanbrainmapping.org/cobidas
+
+## Flow Cytometry
+
+### MIFlowCyt (Minimum Information about a Flow Cytometry Experiment)
+**Purpose:** Flow cytometry experiments
+**Key Requirements:**
+- Experimental overview and purpose
+- Sample characteristics and preparation
+- Instrument information and settings
+- Reagents (antibodies, fluorophores, concentrations)
+- Compensation and controls
+- Gating strategy
+- Data analysis approach
+- Data availability
+
+**Reference:** http://flowcyt.org/
+
+## Ecology and Environmental Science
+
+### MIAPPE (Minimum Information About a Plant Phenotyping Experiment)
+**Purpose:** Plant phenotyping studies
+**Key Requirements:**
+- Investigation and study metadata
+- Biological material information
+- Environmental parameters
+- Experimental design and factors
+- Phenotypic measurements and methods
+- Data file descriptions
+
+**Reference:** https://www.miappe.org/
+
+## Chemistry and Chemical Biology
+
+### MIRIBEL (Minimum Information Reporting in Bio-Nano Experimental Literature)
+**Purpose:** Nanomaterial characterization
+**Key Requirements:**
+- Nanomaterial composition and structure
+- Size, shape, and morphology characterization
+- Surface chemistry and functionalization
+- Purity and stability
+- Experimental conditions
+- Characterization methods
+
+## Quality Assessment and Bias
+
+### CAMARADES (Collaborative Approach to Meta-Analysis and Review of Animal Data from Experimental Studies)
+**Purpose:** Quality assessment for animal studies in systematic reviews
+**Key Items:**
+- Publication in peer-reviewed journal
+- Statement of temperature control
+- Randomization to treatment
+- Blinded assessment of outcome
+- Avoidance of anesthetic with marked intrinsic properties
+- Use of appropriate animal model
+- Sample size calculation
+- Compliance with regulatory requirements
+- Statement of conflict of interest
+- Study pre-registration
+
+### SYRCLE's Risk of Bias Tool
+**Purpose:** Assessing risk of bias in animal intervention studies
+**Domains:**
+- Selection bias (sequence generation, baseline characteristics, allocation concealment)
+- Performance bias (random housing, blinding of personnel)
+- Detection bias (random outcome assessment, blinding of assessors)
+- Attrition bias (incomplete outcome data)
+- Reporting bias (selective outcome reporting)
+- Other sources of bias
+
+## General Principles Across Guidelines
+
+### Common Requirements
+1. **Transparency:** All methods, materials, and analyses fully described
+2. **Reproducibility:** Sufficient detail for independent replication
+3. **Data Availability:** Raw data and analysis code shared or deposited
+4. **Registration:** Studies pre-registered where applicable
+5. **Ethics:** Appropriate approvals and consent documented
+6. **Conflicts of Interest:** Disclosed for all authors
+7. **Statistical Rigor:** Methods appropriate and fully described
+8. **Completeness:** All outcomes reported, including negative results
+
+### Red Flags for Non-Compliance
+- Methods section lacks critical details
+- No mention of following reporting guidelines
+- Data availability statement missing or vague
+- No database accession numbers for omics data
+- No trial registration for clinical studies
+- Sample size not justified
+- Statistical methods inadequately described
+- Missing flow diagrams (CONSORT, PRISMA)
+- Selective reporting of outcomes
+
+## How to Use This Reference
+
+When reviewing a manuscript:
+1. Identify the study type and discipline
+2. Find the relevant reporting guideline(s)
+3. Check if authors mention following the guideline
+4. Verify that key requirements are addressed
+5. Note any missing elements in your review
+6. Suggest the appropriate guideline if not mentioned
+
+Many journals require authors to complete reporting checklists at submission. Reviewers should verify compliance even if a checklist was submitted.
diff --git a/scientific-skills/pptx-posters/SKILL.md b/scientific-skills/pptx-posters/SKILL.md
new file mode 100644
index 0000000..3ba3ef9
--- /dev/null
+++ b/scientific-skills/pptx-posters/SKILL.md
@@ -0,0 +1,958 @@
+---
+name: latex-posters
+description: "Create professional research posters in LaTeX using beamerposter, tikzposter, or baposter. Support for conference presentations, academic posters, and scientific communication. Includes layout design, color schemes, multi-column formats, figure integration, and poster-specific best practices for visual communication."
+allowed-tools: [Read, Write, Edit, Bash]
+---
+
+# LaTeX Research Posters
+
+## Overview
+
+Research posters are a critical medium for scientific communication at conferences, symposia, and academic events. This skill provides comprehensive guidance for creating professional, visually appealing research posters using LaTeX packages. Generate publication-quality posters with proper layout, typography, color schemes, and visual hierarchy.
+
+## When to Use This Skill
+
+This skill should be used when:
+- Creating research posters for conferences, symposia, or poster sessions
+- Designing academic posters for university events or thesis defenses
+- Preparing visual summaries of research for public engagement
+- Converting scientific papers into poster format
+- Creating template posters for research groups or departments
+- Designing posters that comply with specific conference size requirements (A0, A1, 36×48", etc.)
+- Building posters with complex multi-column layouts
+- Integrating figures, tables, equations, and citations in poster format
+
+## Visual Enhancement with Scientific Schematics
+
+**⚠️ MANDATORY: Every research poster MUST include at least 2-3 AI-generated figures using the scientific-schematics skill.**
+
+This is not optional. Posters are primarily visual media - text-heavy posters fail to communicate effectively. Before finalizing any poster:
+1. Generate at minimum TWO schematics or diagrams
+2. Target 3-4 figures for comprehensive posters (methodology flowchart, key results visualization, conceptual framework)
+3. Figures should occupy 40-50% of poster area
+
+**How to generate figures:**
+- Use the **scientific-schematics** skill to generate AI-powered publication-quality diagrams
+- Simply describe your desired diagram in natural language
+- Nano Banana Pro will automatically generate, review, and refine the schematic
+
+**How to generate schematics:**
+```bash
+python scripts/generate_schematic.py "your diagram description" -o figures/output.png
+```
+
+The AI will automatically:
+- Create publication-quality images with proper formatting
+- Review and refine through multiple iterations
+- Ensure accessibility (colorblind-friendly, high contrast)
+- Save outputs in the figures/ directory
+
+**When to add schematics:**
+- Research methodology flowcharts for poster content
+- Conceptual framework diagrams
+- Experimental design visualizations
+- Data analysis pipeline diagrams
+- System architecture diagrams
+- Biological pathway illustrations
+- Any complex concept that benefits from visualization
+
+For detailed guidance on creating schematics, refer to the scientific-schematics skill documentation.
+
+---
+
+## Core Capabilities
+
+### 1. LaTeX Poster Packages
+
+Support for three major LaTeX poster packages, each with distinct advantages. For detailed comparison and package-specific guidance, refer to `references/latex_poster_packages.md`.
+
+**beamerposter**:
+- Extension of the Beamer presentation class
+- Familiar syntax for Beamer users
+- Excellent theme support and customization
+- Best for: Traditional academic posters, institutional branding
+
+**tikzposter**:
+- Modern, flexible design with TikZ integration
+- Built-in color themes and layout templates
+- Extensive customization through TikZ commands
+- Best for: Colorful, modern designs, custom graphics
+
+**baposter**:
+- Box-based layout system
+- Automatic spacing and positioning
+- Professional-looking default styles
+- Best for: Multi-column layouts, consistent spacing
+
+### 2. Poster Layout and Structure
+
+Create effective poster layouts following visual communication principles. For comprehensive layout guidance, refer to `references/poster_layout_design.md`.
+
+**Common Poster Sections**:
+- **Header/Title**: Title, authors, affiliations, logos
+- **Introduction/Background**: Research context and motivation
+- **Methods/Approach**: Methodology and experimental design
+- **Results**: Key findings with figures and data visualizations
+- **Conclusions**: Main takeaways and implications
+- **References**: Key citations (typically abbreviated)
+- **Acknowledgments**: Funding, collaborators, institutions
+
+**Layout Strategies**:
+- **Column-based layouts**: 2-column, 3-column, or 4-column grids
+- **Block-based layouts**: Flexible arrangement of content blocks
+- **Z-pattern flow**: Guide readers through content logically
+- **Visual hierarchy**: Use size, color, and spacing to emphasize key points
+
+### 3. Design Principles for Research Posters
+
+Apply evidence-based design principles for maximum impact. For detailed design guidance, refer to `references/poster_design_principles.md`.
+
+**Typography**:
+- Title: 72-120pt for visibility from distance
+- Section headers: 48-72pt
+- Body text: 24-36pt minimum for readability from 4-6 feet
+- Use sans-serif fonts (Arial, Helvetica, Calibri) for clarity
+- Limit to 2-3 font families maximum
+
+**Color and Contrast**:
+- Use high-contrast color schemes for readability
+- Institutional color palettes for branding
+- Color-blind friendly palettes (avoid red-green combinations)
+- White space is active space—don't overcrowd
+
+**Visual Elements**:
+- High-resolution figures (300 DPI minimum for print)
+- Large, clear labels on all figures
+- Consistent figure styling throughout
+- Strategic use of icons and graphics
+- Balance text with visual content (40-50% visual recommended)
+
+**Content Guidelines**:
+- **Less is more**: 300-800 words total recommended
+- Bullet points over paragraphs for scannability
+- Clear, concise messaging
+- Self-explanatory figures with minimal text explanation
+- QR codes for supplementary materials or online resources
+
+### 4. Standard Poster Sizes
+
+Support for international and conference-specific poster dimensions:
+
+**International Standards**:
+- A0 (841 × 1189 mm / 33.1 × 46.8 inches) - Most common European standard
+- A1 (594 × 841 mm / 23.4 × 33.1 inches) - Smaller format
+- A2 (420 × 594 mm / 16.5 × 23.4 inches) - Compact posters
+
+**North American Standards**:
+- 36 × 48 inches (914 × 1219 mm) - Common US conference size
+- 42 × 56 inches (1067 × 1422 mm) - Large format
+- 48 × 72 inches (1219 × 1829 mm) - Extra large
+
+**Orientation**:
+- Portrait (vertical) - Most common, traditional
+- Landscape (horizontal) - Better for wide content, timelines
+
+### 5. Package-Specific Templates
+
+Provide ready-to-use templates for each major package. Templates available in `assets/` directory.
+
+**beamerposter Templates**:
+- `beamerposter_classic.tex` - Traditional academic style
+- `beamerposter_modern.tex` - Clean, minimal design
+- `beamerposter_colorful.tex` - Vibrant theme with blocks
+
+**tikzposter Templates**:
+- `tikzposter_default.tex` - Standard tikzposter layout
+- `tikzposter_rays.tex` - Modern design with ray theme
+- `tikzposter_wave.tex` - Professional wave-style theme
+
+**baposter Templates**:
+- `baposter_portrait.tex` - Classic portrait layout
+- `baposter_landscape.tex` - Landscape multi-column
+- `baposter_minimal.tex` - Minimalist design
+
+### 6. Figure and Image Integration
+
+Optimize visual content for poster presentations:
+
+**Best Practices**:
+- Use vector graphics (PDF, SVG) when possible for scalability
+- Raster images: minimum 300 DPI at final print size
+- Consistent image styling (borders, captions, sizes)
+- Group related figures together
+- Use subfigures for comparisons
+
+**LaTeX Figure Commands**:
+```latex
+% Include graphics package
+\usepackage{graphicx}
+
+% Simple figure
+\includegraphics[width=0.8\linewidth]{figure.pdf}
+
+% Figure with caption in tikzposter
+\block{Results}{
+ \begin{tikzfigure}
+ \includegraphics[width=0.9\linewidth]{results.png}
+ \end{tikzfigure}
+}
+
+% Multiple subfigures
+\usepackage{subcaption}
+\begin{figure}
+ \begin{subfigure}{0.48\linewidth}
+ \includegraphics[width=\linewidth]{fig1.pdf}
+ \caption{Condition A}
+ \end{subfigure}
+ \begin{subfigure}{0.48\linewidth}
+ \includegraphics[width=\linewidth]{fig2.pdf}
+ \caption{Condition B}
+ \end{subfigure}
+\end{figure}
+```
+
+### 7. Color Schemes and Themes
+
+Provide professional color palettes for various contexts:
+
+**Academic Institution Colors**:
+- Match university or department branding
+- Use official color codes (RGB, CMYK, or LaTeX color definitions)
+
+**Scientific Color Palettes** (color-blind friendly):
+- Viridis: Professional gradient from purple to yellow
+- ColorBrewer: Research-tested palettes for data visualization
+- IBM Color Blind Safe: Accessible corporate palette
+
+**Package-Specific Theme Selection**:
+
+**beamerposter**:
+```latex
+\usetheme{Berlin}
+\usecolortheme{beaver}
+```
+
+**tikzposter**:
+```latex
+\usetheme{Rays}
+\usecolorstyle{Denmark}
+```
+
+**baposter**:
+```latex
+\begin{poster}{
+ background=plain,
+ bgColorOne=white,
+ headerColorOne=blue!70,
+ textborder=rounded
+}
+```
+
+### 8. Typography and Text Formatting
+
+Ensure readability and visual appeal:
+
+**Font Selection**:
+```latex
+% Sans-serif fonts recommended for posters
+\usepackage{helvet} % Helvetica
+\usepackage{avant} % Avant Garde
+\usepackage{sfmath} % Sans-serif math fonts
+
+% Set default to sans-serif
+\renewcommand{\familydefault}{\sfdefault}
+```
+
+**Text Sizing**:
+```latex
+% Adjust text sizes for visibility
+\setbeamerfont{title}{size=\VeryHuge}
+\setbeamerfont{author}{size=\Large}
+\setbeamerfont{institute}{size=\normalsize}
+```
+
+**Emphasis and Highlighting**:
+- Use bold for key terms: `\textbf{important}`
+- Color highlights sparingly: `\textcolor{blue}{highlight}`
+- Boxes for critical information
+- Avoid italics (harder to read from distance)
+
+### 9. QR Codes and Interactive Elements
+
+Enhance poster interactivity for modern conferences:
+
+**QR Code Integration**:
+```latex
+\usepackage{qrcode}
+
+% Link to paper, code repository, or supplementary materials
+\qrcode[height=2cm]{https://github.com/username/project}
+
+% QR code with caption
+\begin{center}
+ \qrcode[height=3cm]{https://doi.org/10.1234/paper}\\
+ \small Scan for full paper
+\end{center}
+```
+
+**Digital Enhancements**:
+- Link to GitHub repositories for code
+- Link to video presentations or demos
+- Link to interactive web visualizations
+- Link to supplementary data or appendices
+
+### 10. Compilation and Output
+
+Generate high-quality PDF output for printing or digital display:
+
+**Compilation Commands**:
+```bash
+# Basic compilation
+pdflatex poster.tex
+
+# With bibliography
+pdflatex poster.tex
+bibtex poster
+pdflatex poster.tex
+pdflatex poster.tex
+
+# For beamer-based posters
+lualatex poster.tex # Better font support
+xelatex poster.tex # Unicode and modern fonts
+```
+
+**Ensuring Full Page Coverage**:
+
+Posters should use the entire page without excessive margins. Configure packages correctly:
+
+**beamerposter - Full Page Setup**:
+```latex
+\documentclass[final,t]{beamer}
+\usepackage[size=a0,scale=1.4,orientation=portrait]{beamerposter}
+
+% Remove default beamer margins
+\setbeamersize{text margin left=0mm, text margin right=0mm}
+
+% Use geometry for precise control
+\usepackage[margin=10mm]{geometry} % 10mm margins all around
+
+% Remove navigation symbols
+\setbeamertemplate{navigation symbols}{}
+
+% Remove footline and headline if not needed
+\setbeamertemplate{footline}{}
+\setbeamertemplate{headline}{}
+```
+
+**tikzposter - Full Page Setup**:
+```latex
+\documentclass[
+ 25pt, % Font scaling
+ a0paper, % Paper size
+ portrait, % Orientation
+ margin=10mm, % Outer margins (minimal)
+ innermargin=15mm, % Space inside blocks
+ blockverticalspace=15mm, % Space between blocks
+ colspace=15mm, % Space between columns
+ subcolspace=8mm % Space between subcolumns
+]{tikzposter}
+
+% This ensures content fills the page
+```
+
+**baposter - Full Page Setup**:
+```latex
+\documentclass[a0paper,portrait,fontscale=0.285]{baposter}
+
+\begin{poster}{
+ grid=false,
+ columns=3,
+ colspacing=1.5em, % Space between columns
+ eyecatcher=true,
+ background=plain,
+ bgColorOne=white,
+ borderColor=blue!50,
+ headerheight=0.12\textheight, % 12% for header
+ textborder=roundedleft,
+ headerborder=closed,
+ boxheaderheight=2em % Consistent box header heights
+}
+% Content here
+\end{poster}
+```
+
+**Common Issues and Fixes**:
+
+**Problem**: Large white margins around poster
+```latex
+% Fix for beamerposter
+\setbeamersize{text margin left=5mm, text margin right=5mm}
+
+% Fix for tikzposter
+\documentclass[..., margin=5mm, innermargin=10mm]{tikzposter}
+
+% Fix for baposter - adjust in document class
+\documentclass[a0paper, margin=5mm]{baposter}
+```
+
+**Problem**: Content doesn't fill vertical space
+```latex
+% Use \vfill between sections to distribute space
+\block{Introduction}{...}
+\vfill
+\block{Methods}{...}
+\vfill
+\block{Results}{...}
+
+% Or manually adjust block spacing
+\vspace{1cm} % Add space between specific blocks
+```
+
+**Problem**: Poster extends beyond page boundaries
+```latex
+% Check total width calculation
+% For 3 columns with spacing:
+% Total = 3×columnwidth + 2×colspace + 2×margins
+% Ensure this equals \paperwidth
+
+% Debug by adding visible page boundary
+\usepackage{eso-pic}
+\AddToShipoutPictureBG{
+ \AtPageLowerLeft{
+ \put(0,0){\framebox(\LenToUnit{\paperwidth},\LenToUnit{\paperheight}){}}
+ }
+}
+```
+
+**Print Preparation**:
+- Generate PDF/X-1a for professional printing
+- Embed all fonts
+- Convert colors to CMYK if required
+- Check resolution of all images (minimum 300 DPI)
+- Add bleed area if required by printer (usually 3-5mm)
+- Verify page size matches requirements exactly
+
+**Digital Display**:
+- RGB color space for screen display
+- Optimize file size for email/web
+- Test readability on different screens
+
+### 11. PDF Review and Quality Control
+
+**CRITICAL**: Always review the generated PDF before printing or presenting. Use this systematic checklist:
+
+**Step 1: Page Size Verification**
+```bash
+# Check PDF dimensions (should match poster size exactly)
+pdfinfo poster.pdf | grep "Page size"
+
+# Expected outputs:
+# A0: 2384 x 3370 points (841 x 1189 mm)
+# 36x48": 2592 x 3456 points
+# A1: 1684 x 2384 points (594 x 841 mm)
+```
+
+**Step 2: Visual Inspection Checklist**
+
+Open PDF at 100% zoom and check:
+
+**Layout and Spacing**:
+- [ ] Content fills entire page (no large white margins)
+- [ ] Consistent spacing between columns
+- [ ] Consistent spacing between blocks/sections
+- [ ] All elements aligned properly (use ruler tool)
+- [ ] No overlapping text or figures
+- [ ] White space evenly distributed
+
+**Typography**:
+- [ ] Title clearly visible and large (72pt+)
+- [ ] Section headers readable (48-72pt)
+- [ ] Body text readable at 100% zoom (24-36pt minimum)
+- [ ] No text cutoff or running off edges
+- [ ] Consistent font usage throughout
+- [ ] All special characters render correctly (symbols, Greek letters)
+
+**Visual Elements**:
+- [ ] All figures display correctly
+- [ ] No pixelated or blurry images
+- [ ] Figure captions present and readable
+- [ ] Colors render as expected (not washed out or too dark)
+- [ ] Logos display clearly
+- [ ] QR codes visible and scannable
+
+**Content Completeness**:
+- [ ] Title and authors complete
+- [ ] All sections present (Intro, Methods, Results, Conclusions)
+- [ ] References included
+- [ ] Contact information visible
+- [ ] Acknowledgments (if applicable)
+- [ ] No placeholder text remaining (Lorem ipsum, TODO, etc.)
+
+**Technical Quality**:
+- [ ] No LaTeX compilation warnings in important areas
+- [ ] All citations resolved (no [?] marks)
+- [ ] All cross-references working
+- [ ] Page boundaries correct (no content cut off)
+
+**Step 3: Reduced-Scale Print Test**
+
+**Essential Pre-Printing Test**:
+```bash
+# Create reduced-size test print (25% of final size)
+# This simulates viewing full poster from ~8-10 feet
+
+# For A0 poster, print on A4 paper (24.7% scale)
+# For 36x48" poster, print on letter paper (~25% scale)
+```
+
+**Print Test Checklist**:
+- [ ] Title readable from 6 feet away
+- [ ] Section headers readable from 4 feet away
+- [ ] Body text readable from 2 feet away
+- [ ] Figures clear and understandable
+- [ ] Colors printed accurately
+- [ ] No obvious design flaws
+
+**Step 4: Digital Quality Checks**
+
+**Font Embedding Verification**:
+```bash
+# Check that all fonts are embedded (required for printing)
+pdffonts poster.pdf
+
+# All fonts should show "yes" in "emb" column
+# If any show "no", recompile with:
+pdflatex -dEmbedAllFonts=true poster.tex
+```
+
+**Image Resolution Check**:
+```bash
+# Extract image information
+pdfimages -list poster.pdf
+
+# Check that all images are at least 300 DPI
+# Formula: DPI = pixels / (inches in poster)
+# For A0 width (33.1"): 300 DPI = 9930 pixels minimum
+```
+
+**File Size Optimization**:
+```bash
+# For email/web, compress if needed (>50MB)
+gs -sDEVICE=pdfwrite -dCompatibilityLevel=1.4 \
+ -dPDFSETTINGS=/printer -dNOPAUSE -dQUIET -dBATCH \
+ -sOutputFile=poster_compressed.pdf poster.pdf
+
+# For printing, keep original (no compression)
+```
+
+**Step 5: Accessibility Check**
+
+**Color Contrast Verification**:
+- [ ] Text-background contrast ratio ≥ 4.5:1 (WCAG AA)
+- [ ] Important elements contrast ratio ≥ 7:1 (WCAG AAA)
+- Test online: https://webaim.org/resources/contrastchecker/
+
+**Color Blindness Simulation**:
+- [ ] View PDF through color blindness simulator
+- [ ] Information not lost with red-green simulation
+- [ ] Use Coblis (color-blindness.com) or similar tool
+
+**Step 6: Content Proofreading**
+
+**Systematic Review**:
+- [ ] Spell-check all text
+- [ ] Verify all author names and affiliations
+- [ ] Check all numbers and statistics for accuracy
+- [ ] Confirm all citations are correct
+- [ ] Review figure labels and captions
+- [ ] Check for typos in headers and titles
+
+**Peer Review**:
+- [ ] Ask colleague to review poster
+- [ ] 30-second test: Can they identify main message?
+- [ ] 5-minute review: Do they understand conclusions?
+- [ ] Note any confusing elements
+
+**Step 7: Technical Validation**
+
+**LaTeX Compilation Log Review**:
+```bash
+# Check for warnings in .log file
+grep -i "warning\|error\|overfull\|underfull" poster.log
+
+# Common issues to fix:
+# - Overfull hbox: Text extending beyond margins
+# - Underfull hbox: Excessive spacing
+# - Missing references: Citations not resolved
+# - Missing figures: Image files not found
+```
+
+**Fix Common Warnings**:
+```latex
+% Overfull hbox (text too wide)
+\usepackage{microtype} % Better spacing
+\sloppy % Allow slightly looser spacing
+\hyphenation{long-word} % Manual hyphenation
+
+% Missing fonts
+\usepackage[T1]{fontenc} % Better font encoding
+
+% Image not found
+% Ensure paths are correct and files exist
+\graphicspath{{./figures/}{./images/}}
+```
+
+**Step 8: Final Pre-Print Checklist**
+
+**Before Sending to Printer**:
+- [ ] PDF size exactly matches requirements (check with pdfinfo)
+- [ ] All fonts embedded (check with pdffonts)
+- [ ] Color mode correct (RGB for screen, CMYK for print if required)
+- [ ] Bleed area added if required (usually 3-5mm)
+- [ ] Crop marks visible if required
+- [ ] Test print completed and reviewed
+- [ ] File naming clear: [LastName]_[Conference]_Poster.pdf
+- [ ] Backup copy saved
+
+**Printing Specifications to Confirm**:
+- [ ] Paper type (matte vs. glossy)
+- [ ] Printing method (inkjet, large format, fabric)
+- [ ] Color profile (provided to printer if required)
+- [ ] Delivery deadline and shipping address
+- [ ] Tube or flat packaging preference
+
+**Digital Presentation Checklist**:
+- [ ] PDF size optimized (<10MB for email)
+- [ ] Tested on multiple PDF viewers (Adobe, Preview, etc.)
+- [ ] Displays correctly on different screens
+- [ ] QR codes tested and functional
+- [ ] Alternative formats prepared (PNG for social media)
+
+**Review Script** (Available in `scripts/review_poster.sh`):
+```bash
+#!/bin/bash
+# Automated poster PDF review script
+
+echo "Poster PDF Quality Check"
+echo "======================="
+
+# Check file exists
+if [ ! -f "$1" ]; then
+ echo "Error: File not found"
+ exit 1
+fi
+
+echo "File: $1"
+echo ""
+
+# Check page size
+echo "1. Page Dimensions:"
+pdfinfo "$1" | grep "Page size"
+echo ""
+
+# Check fonts
+echo "2. Font Embedding:"
+pdffonts "$1" | head -20
+echo ""
+
+# Check file size
+echo "3. File Size:"
+ls -lh "$1" | awk '{print $5}'
+echo ""
+
+# Count pages (should be 1 for poster)
+echo "4. Page Count:"
+pdfinfo "$1" | grep "Pages"
+echo ""
+
+echo "Manual checks required:"
+echo "- Visual inspection at 100% zoom"
+echo "- Reduced-scale print test (25%)"
+echo "- Color contrast verification"
+echo "- Proofreading for typos"
+```
+
+**Common PDF Issues and Solutions**:
+
+| Issue | Cause | Solution |
+|-------|-------|----------|
+| Large white margins | Incorrect margin settings | Reduce margin in documentclass |
+| Content cut off | Exceeds page boundaries | Check total width/height calculations |
+| Blurry images | Low resolution (<300 DPI) | Replace with higher resolution images |
+| Missing fonts | Fonts not embedded | Compile with -dEmbedAllFonts=true |
+| Wrong page size | Incorrect paper size setting | Verify documentclass paper size |
+| Colors look wrong | RGB vs CMYK mismatch | Convert color space for print |
+| File too large (>50MB) | Uncompressed images | Optimize images or compress PDF |
+| QR codes don't work | Too small or low resolution | Minimum 2×2cm, high contrast |
+
+### 11. Common Poster Content Patterns
+
+Effective content organization for different research types:
+
+**Experimental Research Poster**:
+1. Title and authors
+2. Introduction: Problem and hypothesis
+3. Methods: Experimental design (with diagram)
+4. Results: Key findings (2-4 main figures)
+5. Conclusions: Main takeaways (3-5 bullet points)
+6. Future work (optional)
+7. References and acknowledgments
+
+**Computational/Modeling Poster**:
+1. Title and authors
+2. Motivation: Problem statement
+3. Approach: Algorithm or model (with flowchart)
+4. Implementation: Technical details
+5. Results: Performance metrics and comparisons
+6. Applications: Use cases
+7. Code availability (QR code to GitHub)
+8. References
+
+**Review/Survey Poster**:
+1. Title and authors
+2. Scope: Topic overview
+3. Methods: Literature search strategy
+4. Key findings: Main themes (organized by category)
+5. Trends: Visualizations of publication patterns
+6. Gaps: Identified research needs
+7. Conclusions: Summary and implications
+8. References
+
+### 12. Accessibility and Inclusive Design
+
+Design posters that are accessible to diverse audiences:
+
+**Color Blindness Considerations**:
+- Avoid red-green combinations (most common color blindness)
+- Use patterns or shapes in addition to color
+- Test with color-blindness simulators
+- Provide high contrast (WCAG AA standard: 4.5:1 minimum)
+
+**Visual Impairment Accommodations**:
+- Large, clear fonts (minimum 24pt body text)
+- High contrast text and background
+- Clear visual hierarchy
+- Avoid complex textures or patterns in backgrounds
+
+**Language and Content**:
+- Clear, concise language
+- Define acronyms and jargon
+- International audience considerations
+- Consider multilingual QR code options for global conferences
+
+### 13. Poster Presentation Best Practices
+
+Guidance beyond LaTeX for effective poster sessions:
+
+**Content Strategy**:
+- Tell a story, don't just list facts
+- Focus on 1-3 main messages
+- Use visual abstract or graphical summary
+- Leave room for conversation (don't over-explain)
+
+**Physical Presentation Tips**:
+- Bring printed handouts or business cards with QR code
+- Prepare 30-second, 2-minute, and 5-minute verbal summaries
+- Stand to the side, not blocking the poster
+- Engage viewers with open-ended questions
+
+**Digital Backups**:
+- Save poster as PDF on mobile device
+- Prepare digital version for email sharing
+- Create social media-friendly image version
+- Have backup printed copy or digital display option
+
+## Workflow for Poster Creation
+
+### Stage 1: Planning and Content Development
+
+1. **Determine poster requirements**:
+ - Conference size specifications (A0, 36×48", etc.)
+ - Orientation (portrait vs. landscape)
+ - Submission deadlines and format requirements
+
+2. **Develop content outline**:
+ - Identify 1-3 core messages
+ - Select key figures (typically 3-6 main visuals)
+ - Draft concise text for each section (bullet points preferred)
+ - Aim for 300-800 words total
+
+3. **Choose LaTeX package**:
+ - beamerposter: If familiar with Beamer, need institutional themes
+ - tikzposter: For modern, colorful designs with flexibility
+ - baposter: For structured, professional multi-column layouts
+
+### Stage 2: Design and Layout
+
+1. **Select or create template**:
+ - Start with provided templates in `assets/`
+ - Customize color scheme to match branding
+ - Configure page size and orientation
+
+2. **Design layout structure**:
+ - Plan column structure (2, 3, or 4 columns)
+ - Map content flow (typically left-to-right, top-to-bottom)
+ - Allocate space for title (10-15%), content (70-80%), footer (5-10%)
+
+3. **Set typography**:
+ - Configure font sizes for different hierarchy levels
+ - Ensure minimum 24pt body text
+ - Test readability from 4-6 feet distance
+
+### Stage 3: Content Integration
+
+1. **Create poster header**:
+ - Title (concise, descriptive, 10-15 words)
+ - Authors and affiliations
+ - Institution logos (high-resolution)
+ - Conference logo if required
+
+2. **Populate content sections**:
+ - Keep text minimal and scannable
+ - Use bullet points, not paragraphs
+ - Write in active voice
+ - Integrate figures with clear captions
+
+3. **Add visual elements**:
+ - High-resolution figures (300 DPI minimum)
+ - Consistent styling across all figures
+ - Color-coded elements for emphasis
+ - QR codes for supplementary materials
+
+4. **Include references**:
+ - Cite key papers only (5-10 references typical)
+ - Use abbreviated citation style
+ - Consider QR code to full bibliography
+
+### Stage 4: Refinement and Testing
+
+1. **Review and iterate**:
+ - Check for typos and errors
+ - Verify all figures are high resolution
+ - Ensure consistent formatting
+ - Confirm color scheme works well together
+
+2. **Test readability**:
+ - Print at 25% scale and read from 2-3 feet (simulates poster from 8-12 feet)
+ - Check color on different monitors
+ - Verify QR codes function correctly
+ - Ask colleague to review
+
+3. **Optimize for printing**:
+ - Embed all fonts in PDF
+ - Verify image resolution
+ - Check PDF size requirements
+ - Include bleed area if required
+
+### Stage 5: Compilation and Delivery
+
+1. **Compile final PDF**:
+ ```bash
+ pdflatex poster.tex
+ # Or for better font support:
+ lualatex poster.tex
+ ```
+
+2. **Verify output quality**:
+ - Check all elements are visible and correctly positioned
+ - Zoom to 100% and inspect figure quality
+ - Verify colors match expectations
+ - Confirm PDF opens correctly on different viewers
+
+3. **Prepare for printing**:
+ - Export as PDF/X-1a if required
+ - Save backup copies
+ - Get test print on regular paper first
+ - Order professional printing 2-3 days before deadline
+
+4. **Create supplementary materials**:
+ - Save PNG/JPG version for social media
+ - Create handout version (8.5×11" summary)
+ - Prepare digital version for email sharing
+
+## Integration with Other Skills
+
+This skill works effectively with:
+- **Scientific Writing**: For developing poster content from papers
+- **Figure Creation**: For generating high-quality visualizations
+- **Literature Review**: For contextualizing research
+- **Data Analysis**: For creating result figures and charts
+
+## Common Pitfalls to Avoid
+
+**Design Mistakes**:
+- ❌ Too much text (over 1000 words)
+- ❌ Font sizes too small (under 24pt body text)
+- ❌ Low-contrast color combinations
+- ❌ Cluttered layout with no white space
+- ❌ Inconsistent styling across sections
+- ❌ Poor quality or pixelated images
+
+**Content Mistakes**:
+- ❌ No clear narrative or message
+- ❌ Too many research questions or objectives
+- ❌ Overuse of jargon without definitions
+- ❌ Results without context or interpretation
+- ❌ Missing author contact information
+
+**Technical Mistakes**:
+- ❌ Wrong poster dimensions for conference requirements
+- ❌ RGB colors sent to CMYK printer (color shift)
+- ❌ Fonts not embedded in PDF
+- ❌ File size too large for submission portal
+- ❌ QR codes too small or not tested
+
+**Best Practices**:
+- ✅ Follow conference size specifications exactly
+- ✅ Test print at reduced scale before final printing
+- ✅ Use high-contrast, accessible color schemes
+- ✅ Keep text minimal and highly scannable
+- ✅ Include clear contact information and QR codes
+- ✅ Balance text and visuals (40-50% visual content)
+- ✅ Proofread carefully (errors are magnified on posters!)
+
+## Package Installation
+
+Ensure required LaTeX packages are installed:
+
+```bash
+# For TeX Live (Linux/Mac)
+tlmgr install beamerposter tikzposter baposter
+
+# For MiKTeX (Windows)
+# Packages typically auto-install on first use
+
+# Additional recommended packages
+tlmgr install qrcode graphics xcolor tcolorbox subcaption
+```
+
+## Scripts and Automation
+
+Helper scripts available in `scripts/` directory:
+
+- `compile_poster.sh`: Automated compilation with error handling
+- `generate_template.py`: Interactive template generator
+- `resize_images.py`: Batch image optimization for posters
+- `poster_checklist.py`: Pre-submission validation tool
+
+## References
+
+Comprehensive reference files for detailed guidance:
+
+- `references/latex_poster_packages.md`: Detailed comparison of beamerposter, tikzposter, and baposter with examples
+- `references/poster_layout_design.md`: Layout principles, grid systems, and visual flow
+- `references/poster_design_principles.md`: Typography, color theory, visual hierarchy, and accessibility
+- `references/poster_content_guide.md`: Content organization, writing style, and section-specific guidance
+
+## Templates
+
+Ready-to-use poster templates in `assets/` directory:
+
+- beamerposter templates (classic, modern, colorful)
+- tikzposter templates (default, rays, wave, envelope)
+- baposter templates (portrait, landscape, minimal)
+- Example posters from various scientific disciplines
+- Color scheme definitions and institutional templates
+
+Load these templates and customize for your specific research and conference requirements.
+
diff --git a/scientific-skills/pptx-posters/assets/poster_html_template.html b/scientific-skills/pptx-posters/assets/poster_html_template.html
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+
+
+
+
+Research Poster Template - 36x48 inches
+
+
+
+
+
+
+
+
+
+
Introduction
+
+
+
Background: Context about your research problem.
+
Objective: What you aimed to accomplish.
+
+
+
+
Methods
+
+
+
+ - Study design overview
+ - Key methodology
+ - Analysis approach
+
+
+
+
+
+
+
+
Results
+
+
+
Key Finding: Your main result in one sentence
+
+
+
+
+ - Finding 1: Description (p < 0.001)
+ - Finding 2: Description with effect size
+
+
+
+
+
+
+
+
Discussion
+
+
+ - Interpretation of findings
+ - Comparison to prior work
+ - Practical applications
+
+
+
+
+
Conclusions
+
+
+ - Conclusion 1: Clear takeaway
+ - Conclusion 2: Clear takeaway
+ - Future: Next steps
+
+
+
+
+
Acknowledgments
+
+
Funded by Grant #XXX. Thanks to collaborators.
+
+
+
+