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

@@ -8,7 +8,7 @@ license: Proprietary. LICENSE.txt has complete terms
 
 ## Overview
 
-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.
+A .docx file is a ZIP archive containing XML files and resources. Create, edit, or analyze Word documents using text extraction, raw XML access, or redlining workflows. Apply this skill for professional document processing, tracked changes, and content manipulation.
 
 ## Workflow Decision Tree
 

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

@@ -8,7 +8,7 @@ license: Proprietary. LICENSE.txt has complete terms
 
 ## Overview
 
-This guide covers essential PDF processing operations using Python libraries and command-line tools. For advanced features, JavaScript libraries, and detailed examples, see reference.md. If you need to fill out a PDF form, read forms.md and follow its instructions.
+Extract text/tables, create PDFs, merge/split files, fill forms using Python libraries and command-line tools. Apply this skill for programmatic document processing and analysis. For advanced features or form filling, consult reference.md and forms.md.
 
 ## Quick Start
 

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

@@ -8,7 +8,7 @@ license: Proprietary. LICENSE.txt has complete terms
 
 ## Overview
 
-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.
+A .pptx file is a ZIP archive containing XML files and resources. Create, edit, or analyze PowerPoint presentations using text extraction, raw XML access, or html2pptx workflows. Apply this skill for programmatic presentation creation and modification.
 
 ## Reading and analyzing content
 

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

@@ -64,7 +64,7 @@ Unless otherwise stated by the user or existing template
 
 ## Overview
 
-A user may ask you to create, edit, or analyze the contents of an .xlsx file. You have different tools and workflows available for different tasks.
+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.
 
 ## Important Requirements
 

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

@@ -7,7 +7,7 @@ description: "EDA toolkit. Analyze CSV/Excel/JSON/Parquet files, statistical sum
 
 ## Overview
 
-Perform comprehensive exploratory data analysis on datasets of any format. This skill acts as a proficient data scientist, automatically analyzing data to generate meaningful summaries, advanced statistics, visualizations, and actionable insights. All textual outputs are generated as markdown for seamless integration into workflows.
+EDA is a process for discovering patterns, anomalies, and relationships in data. Analyze CSV/Excel/JSON/Parquet files to generate statistical summaries, distributions, correlations, outliers, and visualizations. All outputs are markdown-formatted for integration into workflows.
 
 ## When to Use This Skill
 

scientific-thinking/hypothesis-generation/SKILL.md

@@ -7,7 +7,17 @@ description: "Generate testable hypotheses. Formulate from observations, design
 
 ## Overview
 
-Generate rigorous, evidence-based scientific hypotheses that are testable, falsifiable, and grounded in existing literature. This skill provides a systematic workflow for transforming observations into well-structured hypotheses with experimental designs and testable predictions.
+Hypothesis generation is a systematic process for developing testable explanations. Formulate evidence-based hypotheses from observations, design experiments, explore competing explanations, and develop predictions. Apply this skill for scientific inquiry across domains.
+
+## When to Use This Skill
+
+This skill should be used when:
+- Developing hypotheses from observations or preliminary data
+- Designing experiments to test scientific questions
+- Exploring competing explanations for phenomena
+- Formulating testable predictions for research
+- Conducting literature-based hypothesis generation
+- Planning mechanistic studies across scientific domains
 
 ## Workflow
 

scientific-thinking/peer-review/SKILL.md

@@ -7,7 +7,18 @@ description: "Systematic peer review toolkit. Evaluate methodology, statistics,
 
 ## Overview
 
-This skill enables comprehensive, high-quality peer review of scientific manuscripts across all disciplines. The approach emphasizes constructive criticism, methodological rigor, reproducibility, and clarity, following best practices from leading journals and peer review guidelines.
+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
 
 ## Peer Review Workflow
 

scientific-thinking/scientific-brainstorming/SKILL.md

@@ -7,7 +7,18 @@ description: "Research ideation partner. Generate hypotheses, explore interdisci
 
 ## Overview
 
-Transform into an intelligent scientific thought partner that guides researchers through structured creative ideation. This skill enables deep, conversational brainstorming sessions that help scientists generate novel ideas, make unexpected connections, challenge assumptions, and develop innovative research directions.
+Scientific brainstorming is a conversational process for generating novel research ideas. Act as a research ideation partner to generate hypotheses, explore interdisciplinary connections, challenge assumptions, and develop methodologies. Apply this skill for creative scientific problem-solving.
+
+## When to Use This Skill
+
+This skill should be used when:
+- Generating novel research ideas or directions
+- Exploring interdisciplinary connections and analogies
+- Challenging assumptions in existing research frameworks
+- Developing new methodological approaches
+- Identifying research gaps or opportunities
+- Overcoming creative blocks in problem-solving
+- Brainstorming experimental designs or study plans
 
 ## Core Principles
 

scientific-thinking/scientific-critical-thinking/SKILL.md

@@ -7,7 +7,18 @@ description: "Evaluate research rigor. Assess methodology, experimental design,
 
 ## Overview
 
-Apply systematic, rigorous critical thinking to scientific work using established methodological principles, evidence evaluation frameworks, and logical reasoning. Analyze research methodology, identify biases and fallacies, evaluate statistical claims, assess evidence quality, and provide constructive critique grounded in scientific principles.
+Critical thinking is a systematic process for evaluating scientific rigor. Assess methodology, experimental design, statistical validity, biases, confounding, and evidence quality using GRADE and Cochrane ROB frameworks. Apply this skill for critical analysis of scientific claims.
+
+## When to Use This Skill
+
+This skill should be used when:
+- Evaluating research methodology and experimental design
+- Assessing statistical validity and evidence quality
+- Identifying biases and confounding in studies
+- Reviewing scientific claims and conclusions
+- Conducting systematic reviews or meta-analyses
+- Applying GRADE or Cochrane risk of bias assessments
+- Providing critical analysis of research papers
 
 ## Core Capabilities
 

scientific-thinking/scientific-visualization/SKILL.md

@@ -7,17 +7,11 @@ description: "Create publication figures with matplotlib/seaborn/plotly. Multi-p
 
 ## Overview
 
-This skill provides comprehensive guidance, tools, and best practices for creating publication-ready scientific figures. It covers proper figure composition, colorblind-friendly design, journal-specific requirements, and practical implementation using matplotlib, seaborn, and plotly.
-
-Publication-ready figures must be:
-- **Clear**: Immediately understandable with proper labeling
-- **Accurate**: Truthful data representation without distortion
-- **Accessible**: Interpretable by readers with color vision deficiencies
-- **Professional**: Polished appearance meeting journal standards
+Scientific visualization transforms data into clear, accurate figures for publication. Create journal-ready plots with multi-panel layouts, error bars, significance markers, and colorblind-safe palettes. Export as PDF/EPS/TIFF using matplotlib, seaborn, and plotly for manuscripts.
 
 ## When to Use This Skill
 
-Activate this skill when:
+This skill should be used when:
 - Creating plots or visualizations for scientific manuscripts
 - Preparing figures for journal submission (Nature, Science, Cell, PLOS, etc.)
 - Ensuring figures are colorblind-friendly and accessible

scientific-thinking/scientific-writing/SKILL.md

@@ -7,7 +7,7 @@ description: "Write scientific manuscripts. IMRAD structure, citations (APA/AMA/
 
 ## Overview
 
-Scientific writing is a specialized form of communication that requires precision, clarity, and adherence to established conventions. This skill provides comprehensive guidance for creating high-quality scientific manuscripts, from initial structure to final submission. Whether drafting a research article, review paper, case report, or thesis, this skill ensures writing meets the rigorous standards of academic and scientific publishing.
+Scientific writing is a process for communicating research with precision and clarity. Write manuscripts using IMRAD structure, citations (APA/AMA/Vancouver), figures/tables, and reporting guidelines (CONSORT/STROBE/PRISMA). Apply this skill for research papers and journal submissions.
 
 ## When to Use This Skill
 

scientific-thinking/statistical-analysis/SKILL.md

@@ -7,7 +7,18 @@ description: "Statistical analysis toolkit. Hypothesis tests (t-test, ANOVA, chi
 
 ## Overview
 
-Conduct rigorous, publication-quality statistical analyses with comprehensive assumption checking, effect size calculations, and proper reporting. This skill provides systematic workflows for selecting appropriate statistical tests, validating assumptions, interpreting results, and reporting findings according to academic standards (APA style).
+Statistical analysis is a systematic process for testing hypotheses and quantifying relationships. Conduct hypothesis tests (t-test, ANOVA, chi-square), regression, correlation, and Bayesian analyses with assumption checks and APA reporting. Apply this skill for academic research.
+
+## When to Use This Skill
+
+This skill should be used when:
+- Conducting statistical hypothesis tests (t-tests, ANOVA, chi-square)
+- Performing regression or correlation analyses
+- Running Bayesian statistical analyses
+- Checking statistical assumptions and diagnostics
+- Calculating effect sizes and conducting power analyses
+- Reporting statistical results in APA format
+- Analyzing experimental or observational data for research
 
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