AI Writing Skills

A collection of skills for AI-assisted academic and research writing in medical AI, following the Agent Skills specification.

Skills

1. Protocol Writing (protocol-writing/)

Comprehensive guide for writing clinical research protocols for AI-based diagnostic studies, validation trials, and retrospective analyses.

Includes:

• 16-section protocol structure
• Style guidelines
• Section length reference
• Submission checklist

2. Manuscript Writing (manuscript-writing/)

Full section-by-section guide for writing a medical AI manuscript from scratch.

Includes:

• All sections: Title, Abstract, Introduction, Methods, Results, Discussion
• Threshold reporting requirements for binary classification models
• Table and figure templates
• Submission checklist

3. Manuscript Writing - TRIPOD-AI (manuscript-writing-tripod/)

Guidelines for writing AI papers following TRIPOD+AI reporting standards.

Includes:

• Results section structure
• Table templates with mandatory threshold reporting (Youden Index / binary classification)
• Reviewer-resilience checklist for medical-AI manuscripts
• Label-noise, failure-mode, CONSORT flow, and Table 1 denominator templates
• Typography and abbreviation QC script
• Visual presentation best practices
• Transparency requirements

4. Manuscript Review (manuscript-review/)

Section-by-section checklist for reviewing medical AI manuscripts.

Includes:

• Background, Methods, Results, Tables, Discussion, and Abstract checklists
• Success criteria for each section, including threshold reporting checks for binary classification
• 16-item reviewer-pattern pre-submission checklist for medical-AI papers
• Label-noise, failure-mode, CONSORT flow, and Table 1 denominator templates
• Typography and abbreviation QC script
• Numerical formatting rules
• Forbidden patterns reference

5. CIHR Grant Writing (cihr-grant-writing/)

Section-by-section guide for writing CIHR Project Grant applications.

Includes:

• Full section-by-section structure (Need, Design, Management, General Considerations)
• Weighted scoring rubrics for each subsection
• Fill-in-the-blank templates
• Reference appendices for CIHR-specific language, study type adaptation, and common reviewer critiques

6. CIHR Format Compliance (cihr-format-compliance/)

Pre-submission check that CIHR application PDFs meet the agency’s mechanical format rules and that the right documents are attached.

Includes:

• cihr_pdf_check.py, which reports font, colour, size and margin violations per page
• cihr_roster_check.py, which cross-checks roster name fields and STRAC attestation roles against the attestation forms in the same export
• The LibreOffice font-substitution trap and safe export paths
• Attachment-set rules (STRAC attestations, Scientific Officer notes, the three institution fields)
• Pre-submission checklist

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Directory Structure

Each skill follows the Agent Skills spec format:

ai-writing-skills/
├── protocol-writing/
│   └── SKILL.md
├── manuscript-writing/
│   └── SKILL.md
├── manuscript-writing-tripod/
│   ├── SKILL.md
│   ├── scripts/
│   │   └── typography_qc.py
│   └── templates/
│       ├── consort_flow_table1_template.md
│       ├── failure_mode_panel_template.md
│       ├── failure_mode_panel_template.ipynb
│       └── label_noise_sensitivity_template.md
├── manuscript-review/
│   ├── SKILL.md
│   ├── scripts/
│   │   └── typography_qc.py
│   └── templates/
│       ├── consort_flow_table1_template.md
│       ├── failure_mode_panel_template.md
│       ├── failure_mode_panel_template.ipynb
│       └── label_noise_sensitivity_template.md
├── cihr-grant-writing/
│   ├── SKILL.md
│   └── references/
│       └── APPENDICES.md
├── cihr-format-compliance/
│   ├── SKILL.md
│   └── scripts/
│       ├── cihr_pdf_check.py
│       └── cihr_roster_check.py
└── README.md

Each SKILL.md contains:

• YAML frontmatter with name and description
• Markdown body with full skill instructions

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Installation

Claude Code (Slash Commands)

Install as global slash commands available in every project.

1. Create the commands directory:

mkdir -p ~/.claude/commands

2. Copy each skill’s SKILL.md as a command file:

cp protocol-writing/SKILL.md ~/.claude/commands/protocol-writing.md
cp manuscript-writing-tripod/SKILL.md ~/.claude/commands/manuscript-writing-tripod.md
cp manuscript-review/SKILL.md ~/.claude/commands/manuscript-review.md
cp cihr-grant-writing/SKILL.md ~/.claude/commands/cihr-grant-writing.md

3. Use them anywhere in Claude Code:

/protocol-writing
/manuscript-writing-tripod
/manuscript-review
/cihr-grant-writing

Note: For project-specific commands, place the files in .claude/commands/ inside your project directory instead.

Claude Desktop / Claude.ai (Skills Upload)

1. Package each skill as a ZIP file:

zip -r protocol-writing.zip protocol-writing/
zip -r manuscript-writing-tripod.zip manuscript-writing-tripod/
zip -r manuscript-review.zip manuscript-review/
zip -r cihr-grant-writing.zip cihr-grant-writing/

2. In Claude, go to Settings > Capabilities.

3. Upload each ZIP file as a Skill.

4. Enable the skills and use them in conversations.

Claude Desktop (Projects)

Claude Desktop uses Projects to store reusable instructions and knowledge.

1. Open Claude Desktop and go to Projects (left sidebar).

2. Create a new project (e.g., “Academic Writing Skills”).

3. Add each skill’s SKILL.md as project knowledge:

• Click “Add content” in the project knowledge section
• Select “Add text content” (or drag and drop the file)
• Add each SKILL.md as a separate knowledge entry

4. (Optional) Add project instructions:

You are an academic writing assistant specializing in medical AI research.
When the user asks you to write or review a protocol, manuscript, or grant,
use the relevant skill from the project knowledge to guide your output.
Always follow the structure, style guidelines, and checklists provided.
For manuscript reviews, use the section-by-section checklist approach.

5. Start a new conversation within that project to use the skills.

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ChatGPT / Codex (Custom GPTs or System Prompts)

Option A: Custom GPT (Persistent)

1. Go to https://chat.openai.com/gpts/editor

2. Create a new GPT with the following settings:

• Name: Academic Writing Assistant
• Description: Helps write research protocols, TRIPOD-AI manuscripts, and CIHR grant applications
• Instructions: Paste the following system prompt:

You are an academic writing assistant specializing in medical AI research.
You have access to four writing skills as knowledge files.
When the user asks you to write or review a protocol, use "protocol-writing/SKILL.md".
When the user asks you to write a manuscript, use "manuscript-writing-tripod/SKILL.md".
When the user asks you to review a manuscript, use "manuscript-review/SKILL.md".
When the user asks you to write or review a CIHR grant, use "cihr-grant-writing/SKILL.md".
Always follow the structure, style guidelines, scoring rubrics, and checklists provided in each skill.

3. Upload the 4 SKILL.md files under the “Knowledge” section.

4. Save and use the GPT.

Option B: ChatGPT Projects (Simpler)

1. In ChatGPT, create a new Project (left sidebar).

2. Add each SKILL.md file to the project’s Files section.

3. Add project instructions (same as the system prompt above).

4. Start a conversation within the project.

Option C: Paste into a Single Conversation

If you don’t need persistence, simply paste the contents of the relevant SKILL.md file at the start of any ChatGPT conversation.

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Notion

Option A: Dedicated Database

1. Create a new Notion database called “AI Writing Skills”.

2. Add the following properties:

• Name (Title) – the skill name
• Category (Select) – Protocol / Manuscript / Grant
• Tags (Multi-select) – e.g., TRIPOD-AI, CIHR, Diagnostic AI

3. Create one page per skill:

4. In each page, paste the full contents of the corresponding SKILL.md file.

Option B: Single Page with Toggles

1. Create a new Notion page called “AI Writing Skills”.

2. Add 4 toggle headings:

• Protocol Writing – paste contents of protocol-writing/SKILL.md
• TRIPOD-AI Manuscript Writing – paste contents of manuscript-writing-tripod/SKILL.md
• Manuscript Review – paste contents of manuscript-review/SKILL.md
• CIHR Grant Writing – paste contents of cihr-grant-writing/SKILL.md

Option C: Notion AI Integration

If you have Notion AI enabled:

1. Add the skills as pages (Option A or B above).

2. When using Notion AI, reference the skill page:

• Type @Protocol Writing to link the page
• Then ask Notion AI to “write a protocol following the structure in @Protocol Writing”

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Packaging Skills as ZIP Files

To distribute or share individual skills:

# Package each skill directory into a ZIP
zip -r protocol-writing.zip protocol-writing/
zip -r manuscript-writing-tripod.zip manuscript-writing-tripod/
zip -r manuscript-review.zip manuscript-review/
zip -r cihr-grant-writing.zip cihr-grant-writing/

Each ZIP should contain the skill folder as its root:

protocol-writing.zip
  └── protocol-writing/
      └── SKILL.md

cihr-grant-writing.zip
  └── cihr-grant-writing/
      ├── SKILL.md
      └── references/
          └── APPENDICES.md

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Quick Reference

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License

MIT License - HeartWise.AI

Version

v2.0.0 - Refactored to Agent Skills spec format (SKILL.md + directory structure + ZIP packaging)