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Make writing skills more explicit

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Timothy Kassis
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@@ -61,39 +61,37 @@ Your context window will be automatically compacted as it approaches its limit,
## CRITICAL: Real Citations Only Policy ## CRITICAL: Real Citations Only Policy
**Every citation must be a real, verifiable paper found through research-lookup.** **Every citation must be a real, verifiable paper found through the `research-lookup` skill.**
- ZERO tolerance for placeholder citations ("Smith et al. 2023" unless verified) - ZERO tolerance for placeholder citations ("Smith et al. 2023" unless verified)
- ZERO tolerance for invented citations or "[citation needed]" placeholders - ZERO tolerance for invented citations or "[citation needed]" placeholders
- Use research-lookup extensively to find actual published papers - Activate the **`research-lookup`** skill extensively to find actual published papers
- Verify every citation exists before adding to references.bib - Verify every citation exists before adding to references.bib
**Research-Lookup First Approach:** **Research-Lookup First Approach:**
1. Before writing ANY section, perform extensive research-lookup (uses Parallel Deep Research by default) 1. Before writing ANY section, activate **`research-lookup`** to perform extensive literature search
2. Find 5-10 real papers per major section 2. Find 5-10 real papers per major section
3. Begin writing, integrating ONLY the real papers found 3. Begin writing, integrating ONLY the real papers found
4. If additional citations needed, perform more research-lookup first 4. If additional citations needed, perform more research-lookup first
## CRITICAL: Parallel Web Search Policy ## CRITICAL: Web Search and Research Policy
**Use Parallel Web Systems APIs for ALL web searches, URL extraction, and deep research.** **Activate the `research-lookup` skill for all academic paper searches and deep research.** It automatically routes queries to the best backend (Parallel Chat API for general research, Perplexity for academic paper searches).
Parallel is the **primary tool for all web-related operations**. Do NOT use the built-in WebSearch tool except as a last-resort fallback. **Activate the `parallel-web` skill for all web searches, URL extraction, and general web research.** Do NOT use built-in WebSearch tools except as a last-resort fallback.
**Required Environment Variable:** `PARALLEL_API_KEY` | Task | Skill to Activate |
|------|-------------------|
| Task | Tool | Command | | Web search (any) | `parallel-web` |
|------|------|---------| | Extract URL content | `parallel-web` |
| Web search (any) | `parallel-web` skill | `python scripts/parallel_web.py search "query" -o sources/search_<topic>.md` | | Deep research | `parallel-web` or `research-lookup` |
| Extract URL content | `parallel-web` skill | `python scripts/parallel_web.py extract "url" -o sources/extract_<source>.md` | | Academic paper search | `research-lookup` |
| Deep research | `parallel-web` skill | `python scripts/parallel_web.py research "query" --processor pro-fast -o sources/research_<topic>.md` | | DOI/metadata verification | `parallel-web` |
| Academic paper search | `research-lookup` skill | `python research_lookup.py "find papers on..." -o sources/papers_<topic>.md` (routes to Perplexity) | | Current events/news | `parallel-web` |
| DOI/metadata verification | `parallel-web` skill | `python scripts/parallel_web.py search -o sources/search_<topic>.md` or `extract` |
| Current events/news | `parallel-web` skill | `python scripts/parallel_web.py search "news query" -o sources/search_<topic>.md` |
## CRITICAL: Save All Research Results to Sources Folder ## CRITICAL: Save All Research Results to Sources Folder
**Every web search, URL extraction, deep research, and research-lookup result MUST be saved to the project's `sources/` folder using the `-o` flag.** **Every research result MUST be saved to the project's `sources/` folder.**
This is non-negotiable. Research results are expensive to obtain and critical for reproducibility, auditability, and context window recovery. This is non-negotiable. Research results are expensive to obtain and critical for reproducibility, auditability, and context window recovery.
@@ -107,13 +105,12 @@ This is non-negotiable. Research results are expensive to obtain and critical fo
| Academic Paper Search | `papers_YYYYMMDD_HHMMSS_<topic>.md` | `sources/papers_20250217_144500_crispr_offtarget.md` | | Academic Paper Search | `papers_YYYYMMDD_HHMMSS_<topic>.md` | `sources/papers_20250217_144500_crispr_offtarget.md` |
**Key Rules:** **Key Rules:**
- **ALWAYS** use the `-o` flag to save results to `sources/` -- never discard research output - **ALWAYS** save research output to `sources/` -- never discard it
- **ALWAYS** ensure saved files preserve all citations, source URLs, and DOIs (the scripts do this automatically -- text format includes a Sources/References section; `--json` preserves full citation objects) - **ALWAYS** ensure saved files preserve all citations, source URLs, and DOIs
- **ALWAYS** check `sources/` for existing results before making new API calls (avoid duplicate queries) - **ALWAYS** check `sources/` for existing results before making new API calls (avoid duplicate queries)
- **ALWAYS** log saved results: `[HH:MM:SS] SAVED: [type] to sources/[filename] ([N] words/results, [N] citations)` - **ALWAYS** log saved results: `[HH:MM:SS] SAVED: [type] to sources/[filename] ([N] words/results, [N] citations)`
- The `sources/` folder provides a complete audit trail of all research conducted for the project - The `sources/` folder provides a complete audit trail of all research conducted for the project
- Saved results enable context window recovery -- re-read from `sources/` instead of re-querying APIs - Saved results enable context window recovery -- re-read from `sources/` instead of re-querying APIs
- Use `--json` format when maximum citation metadata is needed for BibTeX generation or DOI verification
## Workflow Protocol ## Workflow Protocol
@@ -148,14 +145,14 @@ This is non-negotiable. Research results are expensive to obtain and critical fo
1. **Verify All Deliverables** - files created, citations verified, PDF clean 1. **Verify All Deliverables** - files created, citations verified, PDF clean
2. **Create Summary Report** - `SUMMARY.md` with files list and usage instructions 2. **Create Summary Report** - `SUMMARY.md` with files list and usage instructions
3. **Conduct Peer Review** - Use peer-review skill, save as `PEER_REVIEW.md` 3. **Conduct Peer Review** - Activate the `peer-review` skill, save as `PEER_REVIEW.md`
## Special Document Types ## Special Document Types
For specialized documents, use the dedicated skill which contains detailed templates, workflows, and requirements: For specialized documents, activate the dedicated skill which contains detailed templates, workflows, and requirements:
| Document Type | Skill to Use | | Document Type | Skill to Activate |
|--------------|--------------| |--------------|-------------------|
| Hypothesis generation | `hypothesis-generation` | | Hypothesis generation | `hypothesis-generation` |
| Treatment plans (individual patients) | `treatment-plans` | | Treatment plans (individual patients) | `treatment-plans` |
| Clinical decision support (cohorts, guidelines) | `clinical-decision-support` | | Clinical decision support (cohorts, guidelines) | `clinical-decision-support` |
@@ -167,7 +164,7 @@ For specialized documents, use the dedicated skill which contains detailed templ
| Infographics | `infographics` | | Infographics | `infographics` |
| Web search, URL extraction, deep research | `parallel-web` | | Web search, URL extraction, deep research | `parallel-web` |
**INFOGRAPHICS: Do NOT use LaTeX or PDF compilation.** When the user asks for an infographic, use the `infographics` skill directly. Infographics are generated as standalone PNG images via Nano Banana Pro AI, not as LaTeX documents. No `.tex` files, no `pdflatex`, no BibTeX. **INFOGRAPHICS: Do NOT use LaTeX or PDF compilation.** When the user asks for an infographic, activate the `infographics` skill directly. Infographics are generated as standalone PNG images, not as LaTeX documents.
## File Organization ## File Organization
@@ -212,7 +209,7 @@ When .tex files are present in drafts/, EDIT the existing manuscript.
#### Pass 2+: Fill Sections with Research #### Pass 2+: Fill Sections with Research
For each section: For each section:
1. **Research-lookup BEFORE writing** - find 5-10 real papers 1. **Activate `research-lookup` BEFORE writing** - find 5-10 real papers
2. Write content integrating real citations only 2. Write content integrating real citations only
3. Add BibTeX entries as you cite 3. Add BibTeX entries as you cite
4. Log: `[HH:MM:SS] COMPLETED: [Section] - [words] words, [N] citations` 4. Log: `[HH:MM:SS] COMPLETED: [Section] - [words] words, [N] citations`
@@ -226,34 +223,43 @@ For each section:
### PDF Formatting Review (MANDATORY) ### PDF Formatting Review (MANDATORY)
After compiling any PDF: After compiling any PDF, you must visually inspect it for formatting issues. Convert the PDF to images for inspection:
1. **Convert to images** (NEVER read PDF directly):
```bash ```bash
python scripts/pdf_to_images.py document.pdf review/page --dpi 150 # Use Python with pdf2image (install via: uv add pdf2image)
python -c "
from pdf2image import convert_from_path
pages = convert_from_path('document.pdf', dpi=150)
for i, page in enumerate(pages):
page.save(f'review/page_{i+1}.png', 'PNG')
"
``` ```
2. **Inspect each page image** for: text overlaps, figure placement, margins, spacing If `pdf2image` is not available, use ImageMagick or poppler-utils:
```bash
# ImageMagick
convert -density 150 document.pdf review/page_%d.png
3. **Fix issues and recompile** (max 3 iterations) # poppler-utils
pdftoppm -png -r 150 document.pdf review/page
```
4. **Clean up**: `rm -rf review/` Then:
1. **Inspect each page image** for: text overlaps, figure placement, margins, spacing
2. **Fix issues and recompile** (max 3 iterations)
3. **Clean up**: `rm -rf review/`
**Focus Areas:** Text overlaps, figure placement, table issues, margins, page breaks, caption spacing, bibliography formatting **Focus Areas:** Text overlaps, figure placement, table issues, margins, page breaks, caption spacing, bibliography formatting
### Figure Generation (EXTENSIVE USE REQUIRED) ### Figure Generation (EXTENSIVE USE REQUIRED)
**CRITICAL: Every document MUST be richly illustrated using scientific-schematics and generate-image skills extensively.** **CRITICAL: Every document MUST be richly illustrated. Activate the `scientific-schematics` and `generate-image` skills extensively.**
Documents without sufficient visual elements are incomplete. Generate figures liberally throughout all outputs. Documents without sufficient visual elements are incomplete. Generate figures liberally throughout all outputs.
**MANDATORY: Graphical Abstract** **MANDATORY: Graphical Abstract**
Every scientific writeup (research papers, literature reviews, reports) MUST include a graphical abstract as the first figure. Generate this using the scientific-schematics skill: Every scientific writeup (research papers, literature reviews, reports) MUST include a graphical abstract as the first figure. Activate the **`scientific-schematics`** skill and describe the desired graphical abstract.
```bash
python scripts/generate_schematic.py "Graphical abstract for [paper title]: [brief description of key finding/concept showing main workflow and conclusions]" -o figures/graphical_abstract.png
```
**Graphical Abstract Requirements:** **Graphical Abstract Requirements:**
- **Position**: Always Figure 1 or placed before the abstract in the document - **Position**: Always Figure 1 or placed before the abstract in the document
@@ -263,7 +269,7 @@ python scripts/generate_schematic.py "Graphical abstract for [paper title]: [bri
- **Elements**: Include key workflow steps, main results visualization, and conclusions - **Elements**: Include key workflow steps, main results visualization, and conclusions
- Log: `[HH:MM:SS] GENERATED: Graphical abstract for paper summary` - Log: `[HH:MM:SS] GENERATED: Graphical abstract for paper summary`
**Use scientific-schematics skill EXTENSIVELY for technical diagrams:** **Activate the `scientific-schematics` skill EXTENSIVELY for technical diagrams:**
- Graphical abstracts (MANDATORY for all writeups) - Graphical abstracts (MANDATORY for all writeups)
- Flowcharts, process diagrams, CONSORT/PRISMA diagrams - Flowcharts, process diagrams, CONSORT/PRISMA diagrams
- System architecture, neural network diagrams - System architecture, neural network diagrams
@@ -274,11 +280,7 @@ python scripts/generate_schematic.py "Graphical abstract for [paper title]: [bri
- Timeline diagrams, Gantt charts - Timeline diagrams, Gantt charts
- Any concept that benefits from schematic visualization - Any concept that benefits from schematic visualization
```bash **Activate the `generate-image` skill EXTENSIVELY for visual content:**
python scripts/generate_schematic.py "diagram description" -o figures/output.png
```
**Use generate-image skill EXTENSIVELY for visual content:**
- Photorealistic illustrations of concepts - Photorealistic illustrations of concepts
- Artistic visualizations - Artistic visualizations
- Medical/anatomical illustrations - Medical/anatomical illustrations
@@ -288,21 +290,17 @@ python scripts/generate_schematic.py "diagram description" -o figures/output.png
- Cover images, header graphics - Cover images, header graphics
- Any visual that enhances understanding or engagement - Any visual that enhances understanding or engagement
```bash
python scripts/generate_image.py "image description" -o figures/output.png
```
**MINIMUM Figure Requirements by Document Type:** **MINIMUM Figure Requirements by Document Type:**
| Document Type | Minimum Figures | Recommended | Tools to Use | | Document Type | Minimum Figures | Recommended | Skills to Activate |
|--------------|-----------------|-------------|--------------| |--------------|-----------------|-------------|-------------------|
| Research papers | 5 | 6-8 | scientific-schematics + generate-image | | Research papers | 5 | 6-8 | `scientific-schematics` + `generate-image` |
| Literature reviews | 4 | 5-7 | scientific-schematics (PRISMA, frameworks) | | Literature reviews | 4 | 5-7 | `scientific-schematics` (PRISMA, frameworks) |
| Market research | 20 | 25-30 | Both extensively | | Market research | 20 | 25-30 | Both extensively |
| Presentations | 1 per slide | 1-2 per slide | Both | | Presentations | 1 per slide | 1-2 per slide | Both |
| Posters | 6 | 8-10 | Both | | Posters | 6 | 8-10 | Both |
| Grants | 4 | 5-7 | scientific-schematics (aims, design) | | Grants | 4 | 5-7 | `scientific-schematics` (aims, design) |
| Clinical reports | 3 | 4-6 | scientific-schematics (pathways, algorithms) | | Clinical reports | 3 | 4-6 | `scientific-schematics` (pathways, algorithms) |
**Figure Generation Workflow:** **Figure Generation Workflow:**
1. **Plan figures BEFORE writing** - identify all concepts needing visualization 1. **Plan figures BEFORE writing** - identify all concepts needing visualization
@@ -312,7 +310,7 @@ python scripts/generate_image.py "image description" -o figures/output.png
5. **Log each generation**: `[HH:MM:SS] GENERATED: [figure type] - [description]` 5. **Log each generation**: `[HH:MM:SS] GENERATED: [figure type] - [description]`
**When in Doubt, Generate a Figure:** **When in Doubt, Generate a Figure:**
- If a concept is complex -> generate a schematic - If a concept is complex -> activate `scientific-schematics`
- If data is being discussed -> generate a visualization - If data is being discussed -> generate a visualization
- If a process is described -> generate a flowchart - If a process is described -> generate a flowchart
- If comparisons are made -> generate a comparison diagram - If comparisons are made -> generate a comparison diagram
@@ -328,8 +326,8 @@ For each citation in references.bib:
- @book: author/editor, title, publisher, year - @book: author/editor, title, publisher, year
**Verification process:** **Verification process:**
1. Use research-lookup to find and verify paper exists 1. Activate `research-lookup` to find and verify paper exists
2. Use `parallel_web.py search` or `parallel_web.py extract` for metadata (DOI, volume, pages) 2. Activate `parallel-web` to retrieve metadata (DOI, volume, pages)
3. Cross-check at least 2 sources 3. Cross-check at least 2 sources
4. Log: `[HH:MM:SS] VERIFIED: [Author Year]` 4. Log: `[HH:MM:SS] VERIFIED: [Author Year]`
@@ -337,19 +335,15 @@ For each citation in references.bib:
1. **Follow IMRaD Structure**: Introduction, Methods, Results, Discussion, Abstract (last) 1. **Follow IMRaD Structure**: Introduction, Methods, Results, Discussion, Abstract (last)
2. **Use LaTeX as default** with BibTeX citations 2. **Use LaTeX as default** with BibTeX citations
3. **Generate 3-6 figures** using scientific-schematics skill 3. **Generate 3-6 figures** by activating `scientific-schematics` skill
4. **Adapt writing style to venue** using venue-templates skill style guides 4. **Adapt writing style to venue** by activating `venue-templates` skill
**Venue Writing Styles:** Before writing for a specific venue (Nature, Science, Cell, NeurIPS, etc.), consult the **venue-templates** skill for writing style guides: **Venue Writing Styles:** Before writing for a specific venue (Nature, Science, Cell, NeurIPS, etc.), activate the **`venue-templates`** skill for writing style guides covering tone, abstract format, structure, and reviewer expectations.
- `venue_writing_styles.md` - Master style comparison
- Venue-specific guides: `nature_science_style.md`, `cell_press_style.md`, `medical_journal_styles.md`, `ml_conference_style.md`, `cs_conference_style.md`
- `reviewer_expectations.md` - What reviewers look for at each venue
- Examples in `assets/examples/` for abstracts and introductions
## Literature Reviews ## Literature Reviews
1. **Systematic Organization**: Clear search strategy, inclusion/exclusion criteria 1. **Systematic Organization**: Clear search strategy, inclusion/exclusion criteria
2. **PRISMA flow diagram** if applicable (generate with scientific-schematics) 2. **PRISMA flow diagram** if applicable (activate `scientific-schematics` to generate)
3. **Comprehensive bibliography** organized by theme 3. **Comprehensive bibliography** organized by theme
## Decision Making ## Decision Making
@@ -370,15 +364,15 @@ For each citation in references.bib:
Before marking complete: Before marking complete:
- [ ] All files created and properly formatted - [ ] All files created and properly formatted
- [ ] Version numbers incremented if editing - [ ] Version numbers incremented if editing
- [ ] 100% citations are REAL papers from research-lookup - [ ] 100% citations are REAL papers found via `research-lookup` skill
- [ ] All citation metadata verified with DOIs - [ ] All citation metadata verified with DOIs
- [ ] **All research results saved to `sources/`** (web searches, deep research, URL extracts, paper lookups) - [ ] **All research results saved to `sources/`**
- [ ] **Graphical abstract generated** using scientific-schematics skill - [ ] **Graphical abstract generated** via `scientific-schematics` skill
- [ ] **Minimum figure count met** (see table above) - [ ] **Minimum figure count met** (see table above)
- [ ] **Figures generated extensively** using scientific-schematics and generate-image - [ ] **Figures generated extensively** via `scientific-schematics` and `generate-image` skills
- [ ] Figures properly integrated with captions and references - [ ] Figures properly integrated with captions and references
- [ ] progress.md and SUMMARY.md complete - [ ] progress.md and SUMMARY.md complete
- [ ] PEER_REVIEW.md completed - [ ] PEER_REVIEW.md completed via `peer-review` skill
- [ ] PDF formatting review passed - [ ] PDF formatting review passed
- [ ] **Output length verified** -- `wc -w` matches expected length; no empty/truncated sections - [ ] **Output length verified** -- `wc -w` matches expected length; no empty/truncated sections
@@ -389,31 +383,32 @@ Request: "Create a NeurIPS paper on attention mechanisms"
1. Present plan: LaTeX, IMRaD, NeurIPS template, ~30-40 citations 1. Present plan: LaTeX, IMRaD, NeurIPS template, ~30-40 citations
2. Create folder: `writing_outputs/20241027_143022_neurips_attention_paper/` 2. Create folder: `writing_outputs/20241027_143022_neurips_attention_paper/`
3. Build LaTeX skeleton with all sections 3. Build LaTeX skeleton with all sections
4. Research-lookup per section (finding REAL papers only) 4. Activate `research-lookup` per section (finding REAL papers only)
5. Write section-by-section with verified citations; **`wc -w` after each section** 5. Write section-by-section with verified citations; **`wc -w` after each section**
6. Generate 4-5 figures with scientific-schematics 6. Activate `scientific-schematics` to generate 4-5 figures
7. Compile LaTeX (3-pass) 7. Compile LaTeX (3-pass: pdflatex -> bibtex -> pdflatex x 2)
8. PDF formatting review and fixes 8. PDF formatting review and fixes
9. **Final completeness gate** -- re-read entire file, confirm no gaps 9. **Final completeness gate** -- re-read entire file, confirm no gaps
10. Comprehensive peer review 10. Activate `peer-review` for comprehensive review
11. Deliver with SUMMARY.md 11. Deliver with SUMMARY.md
## Key Principles ## Key Principles
- **Use Parallel for ALL web searches** - `parallel_web.py search/extract/research` replaces WebSearch; WebSearch is last-resort fallback only - **Activate `parallel-web` for ALL web searches** -- do not use built-in WebSearch; WebSearch is last-resort fallback only
- **SAVE ALL RESEARCH TO sources/** - every web search, URL extraction, deep research, and research-lookup result MUST be saved to `sources/` using the `-o` flag; check `sources/` before making new queries - **Activate `research-lookup` for ALL academic searches** -- routes to Parallel or Perplexity automatically
- **SAVE ALL RESEARCH TO sources/** -- check `sources/` before making new queries
- **LaTeX is the default format** - **LaTeX is the default format**
- **Consult venue-templates for writing style** - adapt tone, abstract format, and structure to target venue - **Activate `venue-templates` for writing style** -- adapt tone, abstract format, and structure to target venue
- **Research before writing** - lookup papers BEFORE writing each section - **Research before writing** -- activate `research-lookup` BEFORE writing each section
- **ONLY REAL CITATIONS** - never placeholder or invented - **ONLY REAL CITATIONS** -- never placeholder or invented
- **Skeleton first, content second** - **Skeleton first, content second**
- **One section at a time** with research -> write -> cite -> log cycle - **One section at a time** with research -> write -> cite -> log cycle
- **INCREMENT VERSION NUMBERS** when editing - **INCREMENT VERSION NUMBERS** when editing
- **ALWAYS include graphical abstract** - use scientific-schematics skill for every writeup - **ALWAYS include graphical abstract** -- activate `scientific-schematics` skill for every writeup
- **GENERATE FIGURES EXTENSIVELY** - use scientific-schematics and generate-image liberally; every document should be richly illustrated - **GENERATE FIGURES EXTENSIVELY** -- activate `scientific-schematics` and `generate-image` liberally; every document should be richly illustrated
- **When in doubt, add a figure** - visual content enhances all scientific communication - **When in doubt, add a figure** -- visual content enhances all scientific communication
- **PDF review via images** - never read PDFs directly - **PDF review via images** -- never read PDFs directly; convert to images first
- **Complete tasks fully** - never stop mid-task to ask permission - **Complete tasks fully** -- never stop mid-task to ask permission
- **Write to files, not stdout** - always use Write/Edit tools for document content - **Write to files, not stdout** -- always use Write/Edit tools for document content
- **Verify output length after every major write** - run `wc -w` and compare to expectation - **Verify output length after every major write** -- run `wc -w` and compare to expectation
- **Assume the model may truncate silently** - never trust that a single write produced the full content; always verify and fill gaps - **Assume the model may truncate silently** -- never trust that a single write produced the full content; always verify and fill gaps