Better adherence to recommendations

.claude-plugin/marketplace.json

@@ -7,7 +7,7 @@
   },
   "metadata": {
     "description": "Claude scientific skills from K-Dense Inc",
-    "version": "1.35.0"
+    "version": "1.35.1"
   },
   "plugins": [
     {

.gitignore

@@ -7,4 +7,5 @@ pyproject.toml
 uv.lock
 
 .venv/
-.python-version
+.python-version
+main.py

scientific-databases/chembl-database/SKILL.md

@@ -11,7 +11,7 @@ Facilitate access to and querying of the ChEMBL database, a manually curated rep
 
 ## When to Use This Skill
 
-Use this skill when queries involve:
+This skill should be used when queries involve:
 
 - **Compound searches**: Finding molecules by name, structure, or properties
 - **Target information**: Retrieving data about proteins, enzymes, or biological targets

scientific-databases/clinicaltrials-database/SKILL.md

@@ -13,7 +13,7 @@ The API is public (no authentication required) with a rate limit of approximatel
 
 ## When to Use This Skill
 
-Use this skill when working with clinical trial data in scenarios such as:
+This skill should be used when working with clinical trial data in scenarios such as:
 
 - **Patient matching** - Finding recruiting trials for specific conditions or patient populations
 - **Research analysis** - Analyzing clinical trial trends, outcomes, or study designs

scientific-databases/clinpgx-database/SKILL.md

@@ -11,7 +11,7 @@ Facilitate access to and querying of ClinPGx (Clinical Pharmacogenomics Database
 
 ## When to Use This Skill
 
-Use this skill when queries involve:
+This skill should be used when queries involve:
 
 - **Gene-drug interactions**: Querying how genetic variants affect drug metabolism, efficacy, or toxicity
 - **CPIC guidelines**: Accessing evidence-based clinical practice guidelines for pharmacogenetics

scientific-databases/cosmic-database/SKILL.md

@@ -11,7 +11,7 @@ COSMIC (Catalogue of Somatic Mutations in Cancer) is the world's largest and mos
 
 ## When to Use This Skill
 
-Use this skill when:
+This skill should be used when:
 - Downloading cancer mutation data from COSMIC
 - Accessing the Cancer Gene Census for curated cancer gene lists
 - Retrieving mutational signature profiles

scientific-databases/fda-database/SKILL.md

@@ -20,7 +20,7 @@ Access comprehensive FDA regulatory data through openFDA, the FDA's initiative t
 
 ## When to Use This Skill
 
-Use this skill when working with:
+This skill should be used when working with:
 - **Drug research**: Safety profiles, adverse events, labeling, approvals, shortages
 - **Medical device surveillance**: Adverse events, recalls, 510(k) clearances, PMA approvals
 - **Food safety**: Recalls, allergen tracking, adverse events, dietary supplements

scientific-databases/gwas-database/SKILL.md

@@ -11,7 +11,7 @@ Facilitate access to and querying of the GWAS Catalog, a comprehensive repositor
 
 ## When to Use This Skill
 
-Use this skill when queries involve:
+This skill should be used when queries involve:
 
 - **Genetic variant associations**: Finding SNPs associated with diseases or traits
 - **SNP lookups**: Retrieving information about specific genetic variants (rs IDs)

scientific-databases/opentargets-database/SKILL.md

@@ -21,7 +21,7 @@ The Open Targets Platform is a comprehensive resource that supports systematic i
 
 ## When to Use This Skill
 
-Use this skill when:
+This skill should be used when:
 
 - **Target discovery:** Finding potential therapeutic targets for a disease
 - **Target assessment:** Evaluating tractability, safety, and druggability of genes

scientific-databases/pubmed-database/SKILL.md

@@ -11,7 +11,7 @@ PubMed is the U.S. National Library of Medicine's comprehensive database providi
 
 ## When to Use This Skill
 
-Use this skill when:
+This skill should be used when:
 - Searching for biomedical or life sciences research articles
 - Constructing complex search queries with Boolean operators, field tags, or MeSH terms
 - Conducting systematic literature reviews or meta-analyses

scientific-databases/zinc-database/SKILL.md

@@ -11,7 +11,7 @@ Facilitate access to and querying of the ZINC database, a freely accessible repo
 
 ## When to Use This Skill
 
-Use this skill when queries involve:
+This skill should be used when queries involve:
 
 - **Virtual screening**: Finding compounds for molecular docking studies
 - **Lead discovery**: Identifying commercially-available compounds for drug development

scientific-integrations/benchling-integration/SKILL.md

@@ -11,7 +11,7 @@ Integrate with Benchling's cloud platform for life sciences R&D, enabling progra
 
 ## When to Use This Skill
 
-Use this skill when:
+This skill should be used when:
 - Working with Benchling's Python SDK or REST API
 - Managing biological sequences (DNA, RNA, proteins) and registry entities
 - Automating inventory operations (samples, containers, locations, transfers)

scientific-integrations/dnanexus-integration/SKILL.md

@@ -17,7 +17,7 @@ DNAnexus is a cloud-based platform for biomedical data analysis, particularly ge
 
 ## When to Use This Skill
 
-Use this skill when working with:
+This skill should be used when working with:
 
 - **App Development**: Creating, building, or modifying DNAnexus apps/applets
 - **Data Management**: Uploading, downloading, searching, or organizing files and records

scientific-integrations/latchbio-integration/SKILL.md

@@ -89,7 +89,7 @@ def my_workflow(input_file: LatchFile) -> LatchFile:
 
 ## When to Use This Skill
 
-Use this skill when encountering any of the following scenarios:
+This skill should be used when encountering any of the following scenarios:
 
 **Workflow Development:**
 - "Create a Latch workflow for RNA-seq analysis"

scientific-packages/astropy/SKILL.md

@@ -11,7 +11,7 @@ Astropy is the community standard Python library for astronomy, providing core f
 
 ## When to Use This Skill
 
-Use this skill when:
+This skill should be used when:
 - Working with FITS files (reading, writing, inspecting, modifying)
 - Performing coordinate transformations between astronomical reference frames
 - Calculating cosmological distances, ages, or other quantities

scientific-packages/biopython/SKILL.md

@@ -11,7 +11,7 @@ BioPython is a comprehensive Python library for computational molecular biology
 
 ## When to Use This Skill
 
-Use this skill when:
+This skill should be used when:
 - Working with biological sequences (DNA, RNA, protein)
 - Reading or writing sequence files (FASTA, GenBank, FASTQ, etc.)
 - Accessing NCBI databases (GenBank, PubMed, Protein, Nucleotide)

scientific-packages/cellxgene-census/SKILL.md

@@ -18,7 +18,7 @@ The Census includes:
 
 ## When to Use This Skill
 
-Use this skill when tasks involve:
+This skill should be used when tasks involve:
 - Querying single-cell expression data by cell type, tissue, or disease
 - Exploring available single-cell datasets and metadata
 - Training machine learning models on single-cell data

scientific-packages/deeptools/SKILL.md

@@ -18,7 +18,7 @@ deepTools is a comprehensive suite of Python command-line tools designed for pro
 
 ## When to Use This Skill
 
-Invoke this skill when users request tasks involving:
+This skill should be used when users request tasks involving:
 
 - **File conversion**: "Convert BAM to bigWig", "generate coverage tracks", "normalize ChIP-seq data"
 - **Quality control**: "check ChIP quality", "compare replicates", "assess sequencing depth", "QC analysis"

scientific-packages/pydeseq2/SKILL.md

@@ -19,7 +19,7 @@ PyDESeq2 is a Python implementation of the DESeq2 method for differential expres
 
 ## When to Use This Skill
 
-Invoke this skill when:
+This skill should be used when:
 - Analyzing bulk RNA-seq count data for differential expression
 - Comparing gene expression between experimental conditions (e.g., treated vs control)
 - Performing multi-factor designs accounting for batch effects or covariates

scientific-packages/pymatgen/SKILL.md

@@ -19,7 +19,7 @@ Pymatgen is a comprehensive Python library for materials analysis that powers th
 
 ## When to Use This Skill
 
-Use this skill when:
+This skill should be used when:
 - Working with crystal structures or molecular systems in materials science
 - Converting between structure file formats (CIF, POSCAR, XYZ, etc.)
 - Analyzing symmetry, space groups, or coordination environments

scientific-packages/pymc/SKILL.md

@@ -11,7 +11,7 @@ PyMC is a Python library for Bayesian modeling and probabilistic programming. Th
 
 ## When to Use This Skill
 
-Use this skill when:
+This skill should be used when:
 - Building Bayesian models (linear/logistic regression, hierarchical models, time series, etc.)
 - Performing MCMC sampling or variational inference
 - Conducting prior/posterior predictive checks

scientific-packages/pytorch-lightning/SKILL.md

@@ -17,7 +17,7 @@ PyTorch Lightning is a deep learning framework that organizes PyTorch code to de
 
 ## When to Use This Skill
 
-Use this skill when:
+This skill should be used when:
 - Building or training deep learning models with PyTorch
 - Converting existing PyTorch code to Lightning structure
 - Setting up distributed training across multiple GPUs or nodes

scientific-packages/reportlab/SKILL.md

@@ -607,7 +607,7 @@ pip install reportlab[renderPM]
 
 ## When to Use This Skill
 
-Invoke this skill when:
+This skill should be used when:
 - Generating PDF documents programmatically
 - Creating invoices, receipts, or billing documents
 - Building reports with tables and charts

scientific-packages/scikit-bio/SKILL.md

@@ -13,7 +13,7 @@ scikit-bio is a comprehensive Python library for working with biological data. P
 
 ## When to Use This Skill
 
-Invoke this skill when the user:
+This skill should be used when the user:
 - Works with biological sequences (DNA, RNA, protein)
 - Needs to read/write biological file formats (FASTA, FASTQ, GenBank, Newick, BIOM, etc.)
 - Performs sequence alignments or searches for motifs

scientific-packages/torch_geometric/SKILL.md

@@ -11,7 +11,7 @@ PyTorch Geometric is a library built on PyTorch that enables development and tra
 
 ## When to Use This Skill
 
-Use this skill when working with:
+This skill should be used when working with:
 - **Graph-based machine learning**: Node classification, graph classification, link prediction
 - **Molecular property prediction**: Drug discovery, chemical property prediction
 - **Social network analysis**: Community detection, influence prediction

scientific-thinking/document-skills/docx/SKILL.md

@@ -8,7 +8,7 @@ license: Proprietary. LICENSE.txt has complete terms
 
 ## Overview
 
-A user may ask you to create, edit, or analyze the contents of a .docx file. A .docx file is essentially a ZIP archive containing XML files and other resources that you can read or edit. You have different tools and workflows available for different tasks.
+This skill supports creating, editing, or analyzing the contents of .docx files. A .docx file is essentially a ZIP archive containing XML files and other resources. Different tools and workflows are available for different tasks.
 
 ## Workflow Decision Tree
 
@@ -31,7 +31,7 @@ Use "Creating a new Word document" workflow
 ## Reading and analyzing content
 
 ### Text extraction
-If you just need to read the text contents of a document, you should convert the document to markdown using pandoc. Pandoc provides excellent support for preserving document structure and can show tracked changes:
+To read the text contents of a document, convert the document to markdown using pandoc. Pandoc provides excellent support for preserving document structure and can show tracked changes:
 
 ```bash
 # Convert document to markdown with tracked changes
@@ -40,7 +40,7 @@ pandoc --track-changes=all path-to-file.docx -o output.md
 ```
 
 ### Raw XML access
-You need raw XML access for: comments, complex formatting, document structure, embedded media, and metadata. For any of these features, you'll need to unpack a document and read its raw XML contents.
+Raw XML access is required for: comments, complex formatting, document structure, embedded media, and metadata. For any of these features, unpack a document and read its raw XML contents.
 
 #### Unpacking a file
 `python ooxml/scripts/unpack.py <office_file> <output_directory>`
@@ -74,7 +74,7 @@ The Document library provides both high-level methods for common operations and
 
 ## Redlining workflow for document review
 
-This workflow allows you to plan comprehensive tracked changes using markdown before implementing them in OOXML. **CRITICAL**: For complete tracked changes, you must implement ALL changes systematically.
+This workflow allows planning comprehensive tracked changes using markdown before implementing them in OOXML. **CRITICAL**: For complete tracked changes, implement ALL changes systematically.
 
 **Batching Strategy**: Group related changes into batches of 3-10 changes. This makes debugging manageable while maintaining efficiency. Test each batch before moving to the next.
 

scientific-thinking/document-skills/pptx/SKILL.md

@@ -8,12 +8,12 @@ license: Proprietary. LICENSE.txt has complete terms
 
 ## Overview
 
-A user may ask you to create, edit, or analyze the contents of a .pptx file. A .pptx file is essentially a ZIP archive containing XML files and other resources that you can read or edit. You have different tools and workflows available for different tasks.
+This skill supports creating, editing, or analyzing the contents of .pptx files. A .pptx file is essentially a ZIP archive containing XML files and other resources. Different tools and workflows are available for different tasks.
 
 ## Reading and analyzing content
 
 ### Text extraction
-If you just need to read the text contents of a presentation, you should convert the document to markdown:
+To read the text contents of a presentation, convert the document to markdown:
 
 ```bash
 # Convert document to markdown
@@ -21,7 +21,7 @@ python -m markitdown path-to-file.pptx
 ```
 
 ### Raw XML access
-You need raw XML access for: comments, speaker notes, slide layouts, animations, design elements, and complex formatting. For any of these features, you'll need to unpack a presentation and read its raw XML contents.
+Raw XML access is required for: comments, speaker notes, slide layouts, animations, design elements, and complex formatting. For any of these features, unpack a presentation and read its raw XML contents.
 
 #### Unpacking a file
 `python ooxml/scripts/unpack.py <office_file> <output_dir>`
@@ -142,7 +142,7 @@ When creating a new PowerPoint presentation from scratch, use the **html2pptx**
 - Negative space as a design element
 
 ### Layout Tips
-**When creating slides with charts or tables:**
+**For slides with charts or tables:**
 - **Two-column layout (PREFERRED)**: Use a header spanning the full width, then two columns below - text/bullets in one column and the featured content in the other. This provides better balance and makes charts/tables more readable. Use flexbox with unequal column widths (e.g., 40%/60% split) to optimize space for each content type.
 - **Full-slide layout**: Let the featured content (chart/table) take up the entire slide for maximum impact and readability
 - **NEVER vertically stack**: Do not place charts/tables below text in a single column - this causes poor readability and layout issues
@@ -170,7 +170,7 @@ When creating a new PowerPoint presentation from scratch, use the **html2pptx**
 
 ## Editing an existing PowerPoint presentation
 
-When edit slides in an existing PowerPoint presentation, you need to work with the raw Office Open XML (OOXML) format. This involves unpacking the .pptx file, editing the XML content, and repacking it.
+To edit slides in an existing PowerPoint presentation, work with the raw Office Open XML (OOXML) format. This involves unpacking the .pptx file, editing the XML content, and repacking it.
 
 ### Workflow
 1. **MANDATORY - READ ENTIRE FILE**: Read [`ooxml.md`](ooxml.md) (~500 lines) completely from start to finish.  **NEVER set any range limits when reading this file.**  Read the full file content for detailed guidance on OOXML structure and editing workflows before any presentation editing.
@@ -181,7 +181,7 @@ When edit slides in an existing PowerPoint presentation, you need to work with t
 
 ## Creating a new PowerPoint presentation **using a template**
 
-When you need to create a presentation that follows an existing template's design, you'll need to duplicate and re-arrange template slides before then replacing placeholder context.
+To create a presentation that follows an existing template's design, duplicate and re-arrange template slides before replacing placeholder context.
 
 ### Workflow
 1. **Extract template text AND create visual thumbnail grid**:
@@ -217,14 +217,14 @@ When you need to create a presentation that follows an existing template's desig
    * Choose safe, text-based layouts for the other slides.
    * **CRITICAL: Match layout structure to actual content**:
      - Single-column layouts: Use for unified narrative or single topic
-     - Two-column layouts: Use ONLY when you have exactly 2 distinct items/concepts
-     - Three-column layouts: Use ONLY when you have exactly 3 distinct items/concepts
-     - Image + text layouts: Use ONLY when you have actual images to insert
+     - Two-column layouts: Use ONLY when there are exactly 2 distinct items/concepts
+     - Three-column layouts: Use ONLY when there are exactly 3 distinct items/concepts
+     - Image + text layouts: Use ONLY when actual images are available to insert
      - Quote layouts: Use ONLY for actual quotes from people (with attribution), never for emphasis
-     - Never use layouts with more placeholders than you have content
-     - If you have 2 items, don't force them into a 3-column layout
-     - If you have 4+ items, consider breaking into multiple slides or using a list format
-   * Count your actual content pieces BEFORE selecting the layout
+     - Never use layouts with more placeholders than available content
+     - If there are 2 items, don't force them into a 3-column layout
+     - If there are 4+ items, consider breaking into multiple slides or using a list format
+   * Count actual content pieces BEFORE selecting the layout
    * Verify each placeholder in the chosen layout will be filled with meaningful content
    * Select one option representing the **best** layout for each content section.
    * Save `outline.md` with content AND template mapping that leverages available designs
@@ -305,9 +305,9 @@ When you need to create a presentation that follows an existing template's desig
 6. **Generate replacement text and save the data to a JSON file**
    Based on the text inventory from the previous step:
    - **CRITICAL**: First verify which shapes exist in the inventory - only reference shapes that are actually present
-   - **VALIDATION**: The replace.py script will validate that all shapes in your replacement JSON exist in the inventory
-     - If you reference a non-existent shape, you'll get an error showing available shapes
-     - If you reference a non-existent slide, you'll get an error indicating the slide doesn't exist
+   - **VALIDATION**: The replace.py script will validate that all shapes in the replacement JSON exist in the inventory
+     - If a non-existent shape is referenced, an error will show available shapes
+     - If a non-existent slide is referenced, an error will indicate the slide doesn't exist
      - All validation errors are shown at once before the script exits
    - **IMPORTANT**: The replace.py script uses inventory.py internally to identify ALL text shapes
    - **AUTOMATIC CLEARING**: ALL text shapes from the inventory will be cleared unless you provide "paragraphs" for them
@@ -317,7 +317,7 @@ When you need to create a presentation that follows an existing template's desig
    - Generate appropriate replacement content for placeholder text
    - Use shape size to determine appropriate content length
    - **CRITICAL**: Include paragraph properties from the original inventory - don't just provide text
-   - **IMPORTANT**: When bullet: true, do NOT include bullet symbols (•, -, *) in text - they're added automatically
+   - **IMPORTANT**: When bullet: true, do NOT include bullet symbols (•, -, *) in text - they are added automatically
    - **ESSENTIAL FORMATTING RULES**:
      - Headers/titles should typically have `"bold": true`
      - List items should have `"bullet": true, "level": 0` (level is required when bullet is true)

scientific-thinking/exploratory-data-analysis/SKILL.md

@@ -11,7 +11,7 @@ Perform comprehensive exploratory data analysis on datasets of any format. This
 
 ## When to Use This Skill
 
-Invoke this skill when:
+This skill should be used when:
 - User provides a data file and requests analysis or exploration
 - User asks to "explore this dataset", "analyze this data", or "what's in this file?"
 - User needs statistical summaries, distributions, or correlations

scientific-thinking/scientific-brainstorming/SKILL.md

@@ -78,8 +78,8 @@ Help the scientist generate a wide range of ideas without judgment. The goal is
 **Interaction style:**
 - Rapid-fire idea generation with the scientist
 - Build on their suggestions with "Yes, and..."
-- Encourage wild ideas explicitly: "What's the most radical approach you can imagine?"
-- Use the references/brainstorming_methods.md file for additional structured techniques
+- Encourage wild ideas explicitly: "What's the most radical approach imaginable?"
+- Consult references/brainstorming_methods.md for additional structured techniques
 
 ### Phase 3: Connection Making
 
@@ -108,10 +108,10 @@ Shift to constructively evaluating the most promising ideas while maintaining cr
 
 **Questions to explore:**
 - "What would it take to actually test this?"
-- "What's the first small experiment you could run?"
-- "What existing data or tools could you leverage?"
+- "What's the first small experiment to run?"
+- "What existing data or tools could be leveraged?"
 - "Who else would need to be involved?"
-- "What's the biggest obstacle, and how might you overcome it?"
+- "What's the biggest obstacle, and how might it be overcome?"
 
 ### Phase 5: Synthesis and Next Steps
 
@@ -163,7 +163,7 @@ Contains detailed descriptions of structured brainstorming methodologies that ca
 - TRIZ principles for inventive problem-solving
 - Biomimicry approaches for nature-inspired solutions
 
-Reference this file when the scientist requests a specific methodology or when the brainstorming session would benefit from a more structured approach.
+Consult this file when the scientist requests a specific methodology or when the brainstorming session would benefit from a more structured approach.
 
 ## Notes
 

scientific-thinking/scientific-writing/SKILL.md

@@ -11,7 +11,7 @@ Scientific writing is a specialized form of communication that requires precisio
 
 ## When to Use This Skill
 
-Invoke this skill when:
+This skill should be used when:
 - Writing or revising any section of a scientific manuscript (abstract, introduction, methods, results, discussion)
 - Structuring a research paper using IMRAD or other standard formats
 - Formatting citations and references in specific styles (APA, AMA, Vancouver, Chicago, IEEE)
@@ -174,8 +174,8 @@ Adapt manuscripts to journal requirements:
 
 Adapt language, terminology, and conventions to match the specific scientific discipline. Each field has established vocabulary, preferred phrasings, and domain-specific conventions that signal expertise and ensure clarity for the target audience.
 
-**Identify Your Field's Linguistic Conventions:**
-- Review terminology used in recent high-impact papers in your target journal
+**Identify Field-Specific Linguistic Conventions:**
+- Review terminology used in recent high-impact papers in the target journal
 - Note field-specific abbreviations, units, and notation systems
 - Identify preferred terms (e.g., "participants" vs. "subjects," "compound" vs. "drug," "specimens" vs. "samples")
 - Observe how methods, organisms, or techniques are typically described
@@ -241,7 +241,7 @@ Adapt language, terminology, and conventions to match the specific scientific di
 **Define Technical Terms Strategically:**
 - Define abbreviations at first use: "messenger RNA (mRNA)"
 - Provide brief explanations for specialized techniques when writing for broader audiences
-- Avoid over-defining terms well-known to your target audience (signals unfamiliarity with field)
+- Avoid over-defining terms well-known to the target audience (signals unfamiliarity with field)
 - Create a glossary if numerous specialized terms are unavoidable
 
 **Maintain Consistency:**
@@ -256,7 +256,7 @@ Adapt language, terminology, and conventions to match the specific scientific di
 
 **Verify Terminology Usage:**
 - Consult field-specific style guides and nomenclature resources
-- Check how terms are used in recent papers from your target journal
+- Check how terms are used in recent papers from the target journal
 - Use domain-specific databases and ontologies (e.g., Gene Ontology, MeSH terms)
 - When uncertain, cite a key reference that establishes terminology
 

scientific-thinking/statistical-analysis/SKILL.md

@@ -48,11 +48,11 @@ Use this decision tree to determine your analysis path:
 ```
 START
 │
-├─ Do you need to SELECT a statistical test?
+├─ Need to SELECT a statistical test?
 │  └─ YES → See "Test Selection Guide"
 │  └─ NO → Continue
 │
-├─ Are you ready to check ASSUMPTIONS?
+├─ Ready to check ASSUMPTIONS?
 │  └─ YES → See "Assumption Checking"
 │  └─ NO → Continue
 │