--- name: scientific-writing description: Core skill for the deep research and writing tool. Write scientific manuscripts in full paragraphs (never bullet points). Use two-stage process with (1) section outlines with key points using research-lookup then (2) convert to flowing prose. IMRAD structure, citations (APA/AMA/Vancouver), figures/tables, reporting guidelines (CONSORT/STROBE/PRISMA), for research papers and journal submissions. allowed-tools: Read Write Edit Bash license: MIT license metadata: skill-author: K-Dense Inc. ---

<!-- ╔══════════════════════════════════════════════════════════════╗ ║ 本文件为开源 Skill 原始文档，收录仅供学习与研究参考 ║ ║ CoPaper.AI 收集整理 | https://copaper.ai ║ ╚══════════════════════════════════════════════════════════════╝

来源仓库: https://github.com/K-Dense-AI/claude-scientific-skills 项目名称: claude-scientific-skills 开源协议: MIT License 收录日期: 2026-04-02

声明: 本文件版权归原作者所有。此处收录旨在为社会科学实证研究者 提供 AI Agent Skills 的集中参考。如有侵权，请联系删除。 -->

# Scientific Writing

## Overview

**This is the core skill for the deep research and writing tool**—combining AI-driven deep research with well-formatted written outputs. Every document produced is backed by comprehensive literature search and verified citations through the research-lookup skill.

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.

**Critical Principle: Always write in full paragraphs with flowing prose. Never submit bullet points in the final manuscript.** Use a two-stage process: first create section outlines with key points using research-lookup, then convert those outlines into complete paragraphs.

## When to Use This Skill

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) - Creating, formatting, or improving figures, tables, and data visualizations - Applying study-specific reporting guidelines (CONSORT for trials, STROBE for observational studies, PRISMA for reviews) - Drafting abstracts that meet journal requirements (structured or unstructured) - Preparing manuscripts for submission to specific journals - Improving writing clarity, conciseness, and precision - Ensuring proper use of field-specific terminology and nomenclature - Addressing reviewer comments and revising manuscripts

## Visual Enhancement with Scientific Schematics

**⚠️ MANDATORY: Every scientific paper MUST include a graphical abstract plus 1-2 additional AI-generated figures using the scientific-schematics skill.**

This is not optional. Scientific papers without visual elements are incomplete. Before finalizing any document: 1. **ALWAYS generate a graphical abstract** as the first visual element 2. Generate at minimum ONE additional schematic or diagram using scientific-schematics 3. Prefer 3-4 total figures for comprehensive papers (graphical abstract + methods flowchart + results visualization + conceptual diagram)

### Graphical Abstract (REQUIRED)

**Every scientific writeup MUST include a graphical abstract.** This is a visual summary of your paper that: - Appears before or immediately after the text abstract - Captures the entire paper's key message in one image - Is suitable for journal table of contents display - Uses landscape orientation (typically 1200x600px)

**Generate the graphical abstract FIRST:** ```bash python scripts/generate_schematic.py "Graphical abstract for [paper title]: [brief description showing workflow from input → methods → key findings → conclusions]" -o figures/graphical_abstract.png ```

**Graphical Abstract Requirements:** - **Content**: Visual summary showing workflow, key methods, main findings, and conclusions - **Style**: Clean, professional, suitable for journal TOC - **Elements**: Include 3-5 key steps/concepts with connecting arrows or flow - **Text**: Minimal labels, large readable fonts - Log: `[HH:MM:SS] GENERATED: Graphical abstract for paper summary`

### Additional Figures (GENERATE EXTENSIVELY)

**⚠️ CRITICAL: Use BOTH scientific-schematics AND generate-image EXTENSIVELY throughout all documents.**

Every document should be richly illustrated. Generate figures liberally - when in doubt, add a visual.

**MINIMUM Figure Requirements:**

| Document Type | Minimum | Recommended | |--------------|---------|-------------| | Research Papers | 5 | 6-8 | | Literature Reviews | 4 | 5-7 | | Market Research | 20 | 25-30 | | Presentations | 1/slide | 1-2/slide | | Posters | 6 | 8-10 | | Grants | 4 | 5-7 | | Clinical Reports | 3 | 4-6 |

**Use scientific-schematics EXTENSIVELY for technical diagrams:** ```bash python scripts/generate_schematic.py "your diagram description" -o figures/output.png ```

- Study design and methodology flowcharts (CONSORT, PRISMA, STROBE) - Conceptual framework diagrams - Experimental workflow illustrations - Data analysis pipeline diagrams - Biological pathway or mechanism diagrams - System architecture visualizations - Neural network architectures - Decision trees, algorithm flowcharts - Comparison matrices, timeline diagrams - Any technical concept that benefits from schematic visualization

**Use generate-image EXTENSIVELY for visual content:** ```bash python scripts/generate_image.py "your image description" -o figures/output.png ```

- Photorealistic illustrations of concepts - Medical/anatomical illustrations - Environmental/ecological scenes - Equipment and lab setup visualizations - Artistic visualizations, infographics - Cover images, header graphics - Product mockups, prototype visualizations - Any visual that enhances understanding or engagement

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 in Doubt, Generate a Figure:** - Complex concept → generate a schematic - Data discussion → generate a visualization - Process description → generate a flowchart - Comparison → generate a comparison diagram - Reader benefit → generate a visual

For detailed guidance, refer to the scientific-schematics and generate-image skill documentation.

---

## Core Capabilities

### 1. Manuscript Structure and Organization

**IMRAD Format**: Guide papers through the standard Introduction, Methods, Results, And Discussion structure used across most scientific disciplines. This includes: - **Introduction**: Establish research context, identify gaps, state objectives - **Methods**: Detail study design, populations, procedures, and analysis approaches - **Results**: Present findings objectively without interpretation - **Discussion**: Interpret results, acknowledge limitations, propose future directions

For detailed guidance on IMRAD structure, refer to `references/imrad_structure.md`.

**Alternative Structures**: Support discipline-specific formats including: - Review articles (narrative, systematic, scoping) - Case reports and case series - Meta-analyses and pooled analyses - Theoretical/modeling papers - Methods papers and protocols

### 2. Section-Specific Writing Guidance

**Abstract Composition**: Craft concise, standalone summaries (100-250 words) that capture the paper's purpose, methods, results, and conclusions. Support both structured abstracts (with labeled sections) and unstructured single-paragraph formats.

**Introduction Development**: Build compelling introductions that: - Establish the research problem's importance - Review relevant literature systematically - Identify knowledge gaps or controversies - State clear research questions or hypotheses - Explain the study's novelty and significance

**Methods Documentation**: Ensure reproducibility through: - Detailed participant/sample descriptions - Clear procedural documentation - Statistical methods with justification - Equipment and materials specifications - Ethical approval and consent statements

**Results Presentation**: Present findings with: - Logical flow from primary to secondary outcomes - Integration with figures and tables - Statistical significance with effect sizes - Objective reporting without interpretation

**Discussion Construction**: Synthesize findings by: - Relating results to research questions - Comparing with existing literature - Acknowledging limitations honestly - Proposing mechanistic explanations - Suggesting practical implications and future research

### 3. Citation and Reference Management

Apply citation styles correctly across disciplines. For comprehensive style guides, refer to `references/citation_styles.md`.

**Major Citation Styles:** - **AMA (American Medical Association)**: Numbered superscript citations, common in medicine - **Vancouver**: Numbered citations in square brackets, biomedical standard - **APA (American Psychological Association)**: Author-date in-text citations, common in social sciences - **Chicago**: Notes-bibliography or author-date, humanities and sciences - **IEEE**: Numbered square brackets, engineering and computer science

**Best Practices:** - Cite primary sources when possible - Include recent literature (last 5-10 years for active fields) - Balance citation distribution across introduction and discussion - Verify all citations against original sources - Use reference management software (Zotero, Mendeley, EndNote)

### 4. Figures and Tables

Create effective data visualizations that enhance comprehension. For detailed best practices, refer to `references/figures_tables.md`.

**When to Use Tables vs. Figures:** - **Tables**: Precise numerical data, complex datasets, multiple variables requiring exact values - **Figures**: Trends, patterns, relationships, comparisons best understood visually

**Design Principles:** - Make each table/figure self-explanatory with complete captions - Use consistent formatting and terminology across all display items - Label all axes, columns, and rows with units - Include sample sizes (n) and statistical annotations - Follow the "one table/figure per 1000 words" guideline - Avoid duplicating information between text, tables, and figures

**Common Figure Types:** - Bar graphs: Comparing discrete categories - Line graphs: Showing trends over time - Scatterplots: Displaying correlations - Box plots: Showing distributions and outliers - Heatmaps: Visualizing matrices and patterns

### 5. Reporting Guidelines by Study Type

Ensure completeness and transparency by following established reporting standards. For comprehensive guideline details, refer to `references/reporting_guidelines.md`.

**Key Guidelines:** - **CONSORT**: Randomized controlled trials - **STROBE**: Observational studies (cohort, case-control, cross-sectional) - **PRISMA**: Systematic reviews and meta-analyses - **STARD**: Diagnostic accuracy studies - **TRIPOD**: Prediction model studies - **ARRIVE**: Animal research - **CARE**: Case reports - **SQUIRE**: Quality improvement studies - **SPIRIT**: Study protocols for clinical trials - **CHEERS**: Economic evaluations

Each guideline provides checklists ensuring all critical methodological elements are reported.

### 6. Writing Principles and Style

Apply fundamental scientific writing principles. For detailed guidance, refer to `references/writing_principles.md`.

**Clarity**: - Use precise, unambiguous language - Define technical terms and abbreviations at first use - Maintain logical flow within and between paragraphs - Use active voice when appropriate for clarity

**Conciseness**: - Eliminate redundant words and phrases - Favor shorter sentences (15-20 words average) - Remove unnecessary qu

--- name: scientific-writing description: Core skill for the deep research and writing tool. Write scientific manuscripts in full paragraphs (never bullet points). Use two-stage process with (1) section outlines with key points using research-lookup then (2) convert to flowing prose. IMRAD structure, citations (APA/AMA/Vancouver), figures/tables, reporting guidelines (CONSORT/STROBE/PRISMA), for research papers and journal submissions. allowed-tools: Read Write Edit Bash license: MIT license metadata: skill-author: K-Dense Inc. ---

<!-- ╔══════════════════════════════════════════════════════════════╗ ║ 本文件为开源 Skill 原始文档，收录仅供学习与研究参考 ║ ║ CoPaper.AI 收集整理 | https://copaper.ai ║ ╚══════════════════════════════════════════════════════════════╝

来源仓库: https://github.com/K-Dense-AI/claude-scientific-skills 项目名称: claude-scientific-skills 开源协议: MIT License 收录日期: 2026-04-02

声明: 本文件版权归原作者所有。此处收录旨在为社会科学实证研究者 提供 AI Agent Skills 的集中参考。如有侵权，请联系删除。 -->

# Scientific Writing

## Overview

**This is the core skill for the deep research and writing tool**—combining AI-driven deep research with well-formatted written outputs. Every document produced is backed by comprehensive literature search and verified citations through the research-lookup skill.

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.

**Critical Principle: Always write in full paragraphs with flowing prose. Never submit bullet points in the final manuscript.** Use a two-stage process: first create section outlines with key points using research-lookup, then convert those outlines into complete paragraphs.

## When to Use This Skill

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) - Creating, formatting, or improving figures, tables, and data visualizations - Applying study-specific reporting guidelines (CONSORT for trials, STROBE for observational studies, PRISMA for reviews) - Drafting abstracts that meet journal requirements (structured or unstructured) - Preparing manuscripts for submission to specific journals - Improving writing clarity, conciseness, and precision - Ensuring proper use of field-specific terminology and nomenclature - Addressing reviewer comments and revising manuscripts

## Visual Enhancement with Scientific Schematics

**⚠️ MANDATORY: Every scientific paper MUST include a graphical abstract plus 1-2 additional AI-generated figures using the scientific-schematics skill.**

This is not optional. Scientific papers without visual elements are incomplete. Before finalizing any document: 1. **ALWAYS generate a graphical abstract** as the first visual element 2. Generate at minimum ONE additional schematic or diagram using scientific-schematics 3. Prefer 3-4 total figures for comprehensive papers (graphical abstract + methods flowchart + results visualization + conceptual diagram)

### Graphical Abstract (REQUIRED)

**Every scientific writeup MUST include a graphical abstract.** This is a visual summary of your paper that: - Appears before or immediately after the text abstract - Captures the entire paper's key message in one image - Is suitable for journal table of contents display - Uses landscape orientation (typically 1200x600px)

**Generate the graphical abstract FIRST:** ```bash python scripts/generate_schematic.py "Graphical abstract for [paper title]: [brief description showing workflow from input → methods → key findings → conclusions]" -o figures/graphical_abstract.png ```

**Graphical Abstract Requirements:** - **Content**: Visual summary showing workflow, key methods, main findings, and conclusions - **Style**: Clean, professional, suitable for journal TOC - **Elements**: Include 3-5 key steps/concepts with connecting arrows or flow - **Text**: Minimal labels, large readable fonts - Log: `[HH:MM:SS] GENERATED: Graphical abstract for paper summary`

### Additional Figures (GENERATE EXTENSIVELY)

**⚠️ CRITICAL: Use BOTH scientific-schematics AND generate-image EXTENSIVELY throughout all documents.**

Every document should be richly illustrated. Generate figures liberally - when in doubt, add a visual.

**MINIMUM Figure Requirements:**

| Document Type | Minimum | Recommended | |--------------|---------|-------------| | Research Papers | 5 | 6-8 | | Literature Reviews | 4 | 5-7 | | Market Research | 20 | 25-30 | | Presentations | 1/slide | 1-2/slide | | Posters | 6 | 8-10 | | Grants | 4 | 5-7 | | Clinical Reports | 3 | 4-6 |

**Use scientific-schematics EXTENSIVELY for technical diagrams:** ```bash python scripts/generate_schematic.py "your diagram description" -o figures/output.png ```

- Study design and methodology flowcharts (CONSORT, PRISMA, STROBE) - Conceptual framework diagrams - Experimental workflow illustrations - Data analysis pipeline diagrams - Biological pathway or mechanism diagrams - System architecture visualizations - Neural network architectures - Decision trees, algorithm flowcharts - Comparison matrices, timeline diagrams - Any technical concept that benefits from schematic visualization

**Use generate-image EXTENSIVELY for visual content:** ```bash python scripts/generate_image.py "your image description" -o figures/output.png ```

- Photorealistic illustrations of concepts - Medical/anatomical illustrations - Environmental/ecological scenes - Equipment and lab setup visualizations - Artistic visualizations, infographics - Cover images, header graphics - Product mockups, prototype visualizations - Any visual that enhances understanding or engagement

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 in Doubt, Generate a Figure:** - Complex concept → generate a schematic - Data discussion → generate a visualization - Process description → generate a flowchart - Comparison → generate a comparison diagram - Reader benefit → generate a visual

For detailed guidance, refer to the scientific-schematics and generate-image skill documentation.

---

## Core Capabilities

### 1. Manuscript Structure and Organization

**IMRAD Format**: Guide papers through the standard Introduction, Methods, Results, And Discussion structure used across most scientific disciplines. This includes: - **Introduction**: Establish research context, identify gaps, state objectives - **Methods**: Detail study design, populations, procedures, and analysis approaches - **Results**: Present findings objectively without interpretation - **Discussion**: Interpret results, acknowledge limitations, propose future directions

For detailed guidance on IMRAD structure, refer to `references/imrad_structure.md`.

**Alternative Structures**: Support discipline-specific formats including: - Review articles (narrative, systematic, scoping) - Case reports and case series - Meta-analyses and pooled analyses - Theoretical/modeling papers - Methods papers and protocols

### 2. Section-Specific Writing Guidance

**Abstract Composition**: Craft concise, standalone summaries (100-250 words) that capture the paper's purpose, methods, results, and conclusions. Support both structured abstracts (with labeled sections) and unstructured single-paragraph formats.

**Introduction Development**: Build compelling introductions that: - Establish the research problem's importance - Review relevant literature systematically - Identify knowledge gaps or controversies - State clear research questions or hypotheses - Explain the study's novelty and significance

**Methods Documentation**: Ensure reproducibility through: - Detailed participant/sample descriptions - Clear procedural documentation - Statistical methods with justification - Equipment and materials specifications - Ethical approval and consent statements

**Results Presentation**: Present findings with: - Logical flow from primary to secondary outcomes - Integration with figures and tables - Statistical significance with effect sizes - Objective reporting without interpretation

**Discussion Construction**: Synthesize findings by: - Relating results to research questions - Comparing with existing literature - Acknowledging limitations honestly - Proposing mechanistic explanations - Suggesting practical implications and future research

### 3. Citation and Reference Management

Apply citation styles correctly across disciplines. For comprehensive style guides, refer to `references/citation_styles.md`.

**Major Citation Styles:** - **AMA (American Medical Association)**: Numbered superscript citations, common in medicine - **Vancouver**: Numbered citations in square brackets, biomedical standard - **APA (American Psychological Association)**: Author-date in-text citations, common in social sciences - **Chicago**: Notes-bibliography or author-date, humanities and sciences - **IEEE**: Numbered square brackets, engineering and computer science

**Best Practices:** - Cite primary sources when possible - Include recent literature (last 5-10 years for active fields) - Balance citation distribution across introduction and discussion - Verify all citations against original sources - Use reference management software (Zotero, Mendeley, EndNote)

### 4. Figures and Tables

Create effective data visualizations that enhance comprehension. For detailed best practices, refer to `references/figures_tables.md`.

**When to Use Tables vs. Figures:** - **Tables**: Precise numerical data, complex datasets, multiple variables requiring exact values - **Figures**: Trends, patterns, relationships, comparisons best understood visually

**Design Principles:** - Make each table/figure self-explanatory with complete captions - Use consistent formatting and terminology across all display items - Label all axes, columns, and rows with units - Include sample sizes (n) and statistical annotations - Follow the "one table/figure per 1000 words" guideline - Avoid duplicating information between text, tables, and figures

**Common Figure Types:** - Bar graphs: Comparing discrete categories - Line graphs: Showing trends over time - Scatterplots: Displaying correlations - Box plots: Showing distributions and outliers - Heatmaps: Visualizing matrices and patterns

### 5. Reporting Guidelines by Study Type

Ensure completeness and transparency by following established reporting standards. For comprehensive guideline details, refer to `references/reporting_guidelines.md`.

**Key Guidelines:** - **CONSORT**: Randomized controlled trials - **STROBE**: Observational studies (cohort, case-control, cross-sectional) - **PRISMA**: Systematic reviews and meta-analyses - **STARD**: Diagnostic accuracy studies - **TRIPOD**: Prediction model studies - **ARRIVE**: Animal research - **CARE**: Case reports - **SQUIRE**: Quality improvement studies - **SPIRIT**: Study protocols for clinical trials - **CHEERS**: Economic evaluations

Each guideline provides checklists ensuring all critical methodological elements are reported.

### 6. Writing Principles and Style

Apply fundamental scientific writing principles. For detailed guidance, refer to `references/writing_principles.md`.

**Clarity**: - Use precise, unambiguous language - Define technical terms and abbreviations at first use - Maintain logical flow within and between paragraphs - Use active voice when appropriate for clarity

**Conciseness**: - Eliminate redundant words and phrases - Favor shorter sentences (15-20 words average) - Remove unnecessary qu

--- name: scientific-writing description: Core skill for the deep research and writing tool. Write scientific manuscripts in full paragraphs (never bullet points). Use two-stage process with (1) section outlines with key points using research-lookup then (2) convert to flowing prose. IMRAD structure, citations (APA/AMA/Vancouver), figures/tables, reporting guidelines (CONSORT/STROBE/PRISMA), for research papers and journal submissions. allowed-tools: Read Write Edit Bash license: MIT license metadata: skill-author: K-Dense Inc. ---

<!-- ╔══════════════════════════════════════════════════════════════╗ ║ 本文件为开源 Skill 原始文档，收录仅供学习与研究参考 ║ ║ CoPaper.AI 收集整理 | https://copaper.ai ║ ╚══════════════════════════════════════════════════════════════╝

来源仓库: https://github.com/K-Dense-AI/claude-scientific-skills 项目名称: claude-scientific-skills 开源协议: MIT License 收录日期: 2026-04-02

声明: 本文件版权归原作者所有。此处收录旨在为社会科学实证研究者 提供 AI Agent Skills 的集中参考。如有侵权，请联系删除。 -->

# Scientific Writing

## Overview

**This is the core skill for the deep research and writing tool**—combining AI-driven deep research with well-formatted written outputs. Every document produced is backed by comprehensive literature search and verified citations through the research-lookup skill.

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.

**Critical Principle: Always write in full paragraphs with flowing prose. Never submit bullet points in the final manuscript.** Use a two-stage process: first create section outlines with key points using research-lookup, then convert those outlines into complete paragraphs.

## When to Use This Skill

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) - Creating, formatting, or improving figures, tables, and data visualizations - Applying study-specific reporting guidelines (CONSORT for trials, STROBE for observational studies, PRISMA for reviews) - Drafting abstracts that meet journal requirements (structured or unstructured) - Preparing manuscripts for submission to specific journals - Improving writing clarity, conciseness, and precision - Ensuring proper use of field-specific terminology and nomenclature - Addressing reviewer comments and revising manuscripts

## Visual Enhancement with Scientific Schematics

**⚠️ MANDATORY: Every scientific paper MUST include a graphical abstract plus 1-2 additional AI-generated figures using the scientific-schematics skill.**

This is not optional. Scientific papers without visual elements are incomplete. Before finalizing any document: 1. **ALWAYS generate a graphical abstract** as the first visual element 2. Generate at minimum ONE additional schematic or diagram using scientific-schematics 3. Prefer 3-4 total figures for comprehensive papers (graphical abstract + methods flowchart + results visualization + conceptual diagram)

### Graphical Abstract (REQUIRED)

**Every scientific writeup MUST include a graphical abstract.** This is a visual summary of your paper that: - Appears before or immediately after the text abstract - Captures the entire paper's key message in one image - Is suitable for journal table of contents display - Uses landscape orientation (typically 1200x600px)

**Generate the graphical abstract FIRST:** ```bash python scripts/generate_schematic.py "Graphical abstract for [paper title]: [brief description showing workflow from input → methods → key findings → conclusions]" -o figures/graphical_abstract.png ```

**Graphical Abstract Requirements:** - **Content**: Visual summary showing workflow, key methods, main findings, and conclusions - **Style**: Clean, professional, suitable for journal TOC - **Elements**: Include 3-5 key steps/concepts with connecting arrows or flow - **Text**: Minimal labels, large readable fonts - Log: `[HH:MM:SS] GENERATED: Graphical abstract for paper summary`

### Additional Figures (GENERATE EXTENSIVELY)

**⚠️ CRITICAL: Use BOTH scientific-schematics AND generate-image EXTENSIVELY throughout all documents.**

Every document should be richly illustrated. Generate figures liberally - when in doubt, add a visual.

**MINIMUM Figure Requirements:**

| Document Type | Minimum | Recommended | |--------------|---------|-------------| | Research Papers | 5 | 6-8 | | Literature Reviews | 4 | 5-7 | | Market Research | 20 | 25-30 | | Presentations | 1/slide | 1-2/slide | | Posters | 6 | 8-10 | | Grants | 4 | 5-7 | | Clinical Reports | 3 | 4-6 |

**Use scientific-schematics EXTENSIVELY for technical diagrams:** ```bash python scripts/generate_schematic.py "your diagram description" -o figures/output.png ```

- Study design and methodology flowcharts (CONSORT, PRISMA, STROBE) - Conceptual framework diagrams - Experimental workflow illustrations - Data analysis pipeline diagrams - Biological pathway or mechanism diagrams - System architecture visualizations - Neural network architectures - Decision trees, algorithm flowcharts - Comparison matrices, timeline diagrams - Any technical concept that benefits from schematic visualization

**Use generate-image EXTENSIVELY for visual content:** ```bash python scripts/generate_image.py "your image description" -o figures/output.png ```

- Photorealistic illustrations of concepts - Medical/anatomical illustrations - Environmental/ecological scenes - Equipment and lab setup visualizations - Artistic visualizations, infographics - Cover images, header graphics - Product mockups, prototype visualizations - Any visual that enhances understanding or engagement

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 in Doubt, Generate a Figure:** - Complex concept → generate a schematic - Data discussion → generate a visualization - Process description → generate a flowchart - Comparison → generate a comparison diagram - Reader benefit → generate a visual

For detailed guidance, refer to the scientific-schematics and generate-image skill documentation.

---

## Core Capabilities

### 1. Manuscript Structure and Organization

**IMRAD Format**: Guide papers through the standard Introduction, Methods, Results, And Discussion structure used across most scientific disciplines. This includes: - **Introduction**: Establish research context, identify gaps, state objectives - **Methods**: Detail study design, populations, procedures, and analysis approaches - **Results**: Present findings objectively without interpretation - **Discussion**: Interpret results, acknowledge limitations, propose future directions

For detailed guidance on IMRAD structure, refer to `references/imrad_structure.md`.

**Alternative Structures**: Support discipline-specific formats including: - Review articles (narrative, systematic, scoping) - Case reports and case series - Meta-analyses and pooled analyses - Theoretical/modeling papers - Methods papers and protocols

### 2. Section-Specific Writing Guidance

**Abstract Composition**: Craft concise, standalone summaries (100-250 words) that capture the paper's purpose, methods, results, and conclusions. Support both structured abstracts (with labeled sections) and unstructured single-paragraph formats.

**Introduction Development**: Build compelling introductions that: - Establish the research problem's importance - Review relevant literature systematically - Identify knowledge gaps or controversies - State clear research questions or hypotheses - Explain the study's novelty and significance

**Methods Documentation**: Ensure reproducibility through: - Detailed participant/sample descriptions - Clear procedural documentation - Statistical methods with justification - Equipment and materials specifications - Ethical approval and consent statements

**Results Presentation**: Present findings with: - Logical flow from primary to secondary outcomes - Integration with figures and tables - Statistical significance with effect sizes - Objective reporting without interpretation

**Discussion Construction**: Synthesize findings by: - Relating results to research questions - Comparing with existing literature - Acknowledging limitations honestly - Proposing mechanistic explanations - Suggesting practical implications and future research

### 3. Citation and Reference Management

Apply citation styles correctly across disciplines. For comprehensive style guides, refer to `references/citation_styles.md`.

**Major Citation Styles:** - **AMA (American Medical Association)**: Numbered superscript citations, common in medicine - **Vancouver**: Numbered citations in square brackets, biomedical standard - **APA (American Psychological Association)**: Author-date in-text citations, common in social sciences - **Chicago**: Notes-bibliography or author-date, humanities and sciences - **IEEE**: Numbered square brackets, engineering and computer science

**Best Practices:** - Cite primary sources when possible - Include recent literature (last 5-10 years for active fields) - Balance citation distribution across introduction and discussion - Verify all citations against original sources - Use reference management software (Zotero, Mendeley, EndNote)

### 4. Figures and Tables

Create effective data visualizations that enhance comprehension. For detailed best practices, refer to `references/figures_tables.md`.

**When to Use Tables vs. Figures:** - **Tables**: Precise numerical data, complex datasets, multiple variables requiring exact values - **Figures**: Trends, patterns, relationships, comparisons best understood visually

**Design Principles:** - Make each table/figure self-explanatory with complete captions - Use consistent formatting and terminology across all display items - Label all axes, columns, and rows with units - Include sample sizes (n) and statistical annotations - Follow the "one table/figure per 1000 words" guideline - Avoid duplicating information between text, tables, and figures

**Common Figure Types:** - Bar graphs: Comparing discrete categories - Line graphs: Showing trends over time - Scatterplots: Displaying correlations - Box plots: Showing distributions and outliers - Heatmaps: Visualizing matrices and patterns

### 5. Reporting Guidelines by Study Type

Ensure completeness and transparency by following established reporting standards. For comprehensive guideline details, refer to `references/reporting_guidelines.md`.

**Key Guidelines:** - **CONSORT**: Randomized controlled trials - **STROBE**: Observational studies (cohort, case-control, cross-sectional) - **PRISMA**: Systematic reviews and meta-analyses - **STARD**: Diagnostic accuracy studies - **TRIPOD**: Prediction model studies - **ARRIVE**: Animal research - **CARE**: Case reports - **SQUIRE**: Quality improvement studies - **SPIRIT**: Study protocols for clinical trials - **CHEERS**: Economic evaluations

Each guideline provides checklists ensuring all critical methodological elements are reported.

### 6. Writing Principles and Style

Apply fundamental scientific writing principles. For detailed guidance, refer to `references/writing_principles.md`.

**Clarity**: - Use precise, unambiguous language - Define technical terms and abbreviations at first use - Maintain logical flow within and between paragraphs - Use active voice when appropriate for clarity

**Conciseness**: - Eliminate redundant words and phrases - Favor shorter sentences (15-20 words average) - Remove unnecessary qu

--- name: scientific-writing description: Core skill for the deep research and writing tool. Write scientific manuscripts in full paragraphs (never bullet points). Use two-stage process with (1) section outlines with key points using research-lookup then (2) convert to flowing prose. IMRAD structure, citations (APA/AMA/Vancouver), figures/tables, reporting guidelines (CONSORT/STROBE/PRISMA), for research papers and journal submissions. allowed-tools: Read Write Edit Bash license: MIT license metadata: skill-author: K-Dense Inc. ---

<!-- ╔══════════════════════════════════════════════════════════════╗ ║ 本文件为开源 Skill 原始文档，收录仅供学习与研究参考 ║ ║ CoPaper.AI 收集整理 | https://copaper.ai ║ ╚══════════════════════════════════════════════════════════════╝

来源仓库: https://github.com/K-Dense-AI/claude-scientific-skills 项目名称: claude-scientific-skills 开源协议: MIT License 收录日期: 2026-04-02

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# Scientific Writing

## Overview

**This is the core skill for the deep research and writing tool**—combining AI-driven deep research with well-formatted written outputs. Every document produced is backed by comprehensive literature search and verified citations through the research-lookup skill.

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.

**Critical Principle: Always write in full paragraphs with flowing prose. Never submit bullet points in the final manuscript.** Use a two-stage process: first create section outlines with key points using research-lookup, then convert those outlines into complete paragraphs.

## When to Use This Skill

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) - Creating, formatting, or improving figures, tables, and data visualizations - Applying study-specific reporting guidelines (CONSORT for trials, STROBE for observational studies, PRISMA for reviews) - Drafting abstracts that meet journal requirements (structured or unstructured) - Preparing manuscripts for submission to specific journals - Improving writing clarity, conciseness, and precision - Ensuring proper use of field-specific terminology and nomenclature - Addressing reviewer comments and revising manuscripts

## Visual Enhancement with Scientific Schematics

**⚠️ MANDATORY: Every scientific paper MUST include a graphical abstract plus 1-2 additional AI-generated figures using the scientific-schematics skill.**

This is not optional. Scientific papers without visual elements are incomplete. Before finalizing any document: 1. **ALWAYS generate a graphical abstract** as the first visual element 2. Generate at minimum ONE additional schematic or diagram using scientific-schematics 3. Prefer 3-4 total figures for comprehensive papers (graphical abstract + methods flowchart + results visualization + conceptual diagram)

### Graphical Abstract (REQUIRED)

**Every scientific writeup MUST include a graphical abstract.** This is a visual summary of your paper that: - Appears before or immediately after the text abstract - Captures the entire paper's key message in one image - Is suitable for journal table of contents display - Uses landscape orientation (typically 1200x600px)

**Generate the graphical abstract FIRST:** ```bash python scripts/generate_schematic.py "Graphical abstract for [paper title]: [brief description showing workflow from input → methods → key findings → conclusions]" -o figures/graphical_abstract.png ```

**Graphical Abstract Requirements:** - **Content**: Visual summary showing workflow, key methods, main findings, and conclusions - **Style**: Clean, professional, suitable for journal TOC - **Elements**: Include 3-5 key steps/concepts with connecting arrows or flow - **Text**: Minimal labels, large readable fonts - Log: `[HH:MM:SS] GENERATED: Graphical abstract for paper summary`

### Additional Figures (GENERATE EXTENSIVELY)

**⚠️ CRITICAL: Use BOTH scientific-schematics AND generate-image EXTENSIVELY throughout all documents.**

Every document should be richly illustrated. Generate figures liberally - when in doubt, add a visual.

**MINIMUM Figure Requirements:**

| Document Type | Minimum | Recommended | |--------------|---------|-------------| | Research Papers | 5 | 6-8 | | Literature Reviews | 4 | 5-7 | | Market Research | 20 | 25-30 | | Presentations | 1/slide | 1-2/slide | | Posters | 6 | 8-10 | | Grants | 4 | 5-7 | | Clinical Reports | 3 | 4-6 |

**Use scientific-schematics EXTENSIVELY for technical diagrams:** ```bash python scripts/generate_schematic.py "your diagram description" -o figures/output.png ```

- Study design and methodology flowcharts (CONSORT, PRISMA, STROBE) - Conceptual framework diagrams - Experimental workflow illustrations - Data analysis pipeline diagrams - Biological pathway or mechanism diagrams - System architecture visualizations - Neural network architectures - Decision trees, algorithm flowcharts - Comparison matrices, timeline diagrams - Any technical concept that benefits from schematic visualization

**Use generate-image EXTENSIVELY for visual content:** ```bash python scripts/generate_image.py "your image description" -o figures/output.png ```

- Photorealistic illustrations of concepts - Medical/anatomical illustrations - Environmental/ecological scenes - Equipment and lab setup visualizations - Artistic visualizations, infographics - Cover images, header graphics - Product mockups, prototype visualizations - Any visual that enhances understanding or engagement

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 in Doubt, Generate a Figure:** - Complex concept → generate a schematic - Data discussion → generate a visualization - Process description → generate a flowchart - Comparison → generate a comparison diagram - Reader benefit → generate a visual

For detailed guidance, refer to the scientific-schematics and generate-image skill documentation.

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## Core Capabilities

### 1. Manuscript Structure and Organization

**IMRAD Format**: Guide papers through the standard Introduction, Methods, Results, And Discussion structure used across most scientific disciplines. This includes: - **Introduction**: Establish research context, identify gaps, state objectives - **Methods**: Detail study design, populations, procedures, and analysis approaches - **Results**: Present findings objectively without interpretation - **Discussion**: Interpret results, acknowledge limitations, propose future directions

For detailed guidance on IMRAD structure, refer to `references/imrad_structure.md`.

**Alternative Structures**: Support discipline-specific formats including: - Review articles (narrative, systematic, scoping) - Case reports and case series - Meta-analyses and pooled analyses - Theoretical/modeling papers - Methods papers and protocols

### 2. Section-Specific Writing Guidance

**Abstract Composition**: Craft concise, standalone summaries (100-250 words) that capture the paper's purpose, methods, results, and conclusions. Support both structured abstracts (with labeled sections) and unstructured single-paragraph formats.

**Introduction Development**: Build compelling introductions that: - Establish the research problem's importance - Review relevant literature systematically - Identify knowledge gaps or controversies - State clear research questions or hypotheses - Explain the study's novelty and significance

**Methods Documentation**: Ensure reproducibility through: - Detailed participant/sample descriptions - Clear procedural documentation - Statistical methods with justification - Equipment and materials specifications - Ethical approval and consent statements

**Results Presentation**: Present findings with: - Logical flow from primary to secondary outcomes - Integration with figures and tables - Statistical significance with effect sizes - Objective reporting without interpretation

**Discussion Construction**: Synthesize findings by: - Relating results to research questions - Comparing with existing literature - Acknowledging limitations honestly - Proposing mechanistic explanations - Suggesting practical implications and future research

### 3. Citation and Reference Management

Apply citation styles correctly across disciplines. For comprehensive style guides, refer to `references/citation_styles.md`.

**Major Citation Styles:** - **AMA (American Medical Association)**: Numbered superscript citations, common in medicine - **Vancouver**: Numbered citations in square brackets, biomedical standard - **APA (American Psychological Association)**: Author-date in-text citations, common in social sciences - **Chicago**: Notes-bibliography or author-date, humanities and sciences - **IEEE**: Numbered square brackets, engineering and computer science

**Best Practices:** - Cite primary sources when possible - Include recent literature (last 5-10 years for active fields) - Balance citation distribution across introduction and discussion - Verify all citations against original sources - Use reference management software (Zotero, Mendeley, EndNote)

### 4. Figures and Tables

Create effective data visualizations that enhance comprehension. For detailed best practices, refer to `references/figures_tables.md`.

**When to Use Tables vs. Figures:** - **Tables**: Precise numerical data, complex datasets, multiple variables requiring exact values - **Figures**: Trends, patterns, relationships, comparisons best understood visually

**Design Principles:** - Make each table/figure self-explanatory with complete captions - Use consistent formatting and terminology across all display items - Label all axes, columns, and rows with units - Include sample sizes (n) and statistical annotations - Follow the "one table/figure per 1000 words" guideline - Avoid duplicating information between text, tables, and figures

**Common Figure Types:** - Bar graphs: Comparing discrete categories - Line graphs: Showing trends over time - Scatterplots: Displaying correlations - Box plots: Showing distributions and outliers - Heatmaps: Visualizing matrices and patterns

### 5. Reporting Guidelines by Study Type

Ensure completeness and transparency by following established reporting standards. For comprehensive guideline details, refer to `references/reporting_guidelines.md`.

**Key Guidelines:** - **CONSORT**: Randomized controlled trials - **STROBE**: Observational studies (cohort, case-control, cross-sectional) - **PRISMA**: Systematic reviews and meta-analyses - **STARD**: Diagnostic accuracy studies - **TRIPOD**: Prediction model studies - **ARRIVE**: Animal research - **CARE**: Case reports - **SQUIRE**: Quality improvement studies - **SPIRIT**: Study protocols for clinical trials - **CHEERS**: Economic evaluations

Each guideline provides checklists ensuring all critical methodological elements are reported.

### 6. Writing Principles and Style

Apply fundamental scientific writing principles. For detailed guidance, refer to `references/writing_principles.md`.

**Clarity**: - Use precise, unambiguous language - Define technical terms and abbreviations at first use - Maintain logical flow within and between paragraphs - Use active voice when appropriate for clarity

**Conciseness**: - Eliminate redundant words and phrases - Favor shorter sentences (15-20 words average) - Remove unnecessary qu