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clinical-trial-protocol-skill

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by anthropic · part of anthropics/life-sciences

Generate clinical trial protocols for medical devices or drugs. This skill should be used when users say "Create a clinical trial protocol", "Generate protocol…

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🧩 One of 6 skills in the anthropics/life-sciences package — works on its own, and pairs well with its siblings.

This is the playbook your agent receives when the skill activates — you don't need to read it to use the skill, but it's here to audit before installing.

name: clinical-trial-protocol-skill description: Generate clinical trial protocols for medical devices or drugs. This skill should be used when users say "Create a clinical trial protocol", "Generate protocol for [device/drug]", "Help me design a clinical study", "Research similar trials for [intervention]", or when developing FDA submission documentation for investigational products.

Clinical Trial Protocol Skill

⚠️ EXECUTION CONTROL - READ THIS FIRST

CRITICAL: This orchestrator follows a SIMPLE START approach:

  1. Display the welcome message FIRST (shown in "Startup: Welcome and Confirmation" section below)
  2. Ask user to confirm they're ready to proceed - Wait for confirmation (yes/no)
  3. Jump directly into Full Workflow Logic - Automatically run subskills sequentially
  4. Do NOT pre-read subskill files - Subskills are loaded on-demand only when their step executes

Why this matters:

  • Pre-reading all subskills wastes context and memory
  • Subskills should only load when actually needed during execution
  • Workflow automatically handles resuming from existing waypoints

Overview

This skill generates clinical trial protocols for medical devices or drugs using a modular, waypoint-based architecture

What This Skill Does

Starting with an intervention idea (device or drug), this orchestrated workflow offers two modes:

🔬 Research Only Mode (Steps 0-1): 0. Initialize Intervention - Collect device or drug information

  1. Research Similar Protocols - Find similar trials, FDA guidance, and published protocols
    • Deliverable: Comprehensive research summary as formatted .md artifact

📄 Full Protocol Mode (Steps 0-5): 0. Initialize Intervention - Collect device or drug information

  1. Research Similar Protocols - Find similar trials, FDA guidance, and published protocols
  2. Protocol Foundation - Generate protocol sections 1-6 (foundation, design, population)
  3. Protocol Intervention - Generate protocol sections 7-8 (intervention details)
  4. Protocol Operations - Generate protocol sections 9-12 (assessments, statistics, operations)
  5. Generate Protocol - Create professional file ready for stakeholder review

Architecture

Waypoint-Based Design

All analysis data is stored in waypoints/ directory as JSON/markdown files:

waypoints/
├── intervention_metadata.json           # Intervention info, status, initial context
├── 01_clinical_research_summary.json   # Similar trials, FDA guidance, recommendations
├── 02_protocol_foundation.md            # Protocol sections 1-6 (Step 2)
├── 03_protocol_intervention.md          # Protocol sections 7-8 (Step 3)
├── 04_protocol_operations.md            # Protocol sections 9-12 (Step 4)
├── 02_protocol_draft.md                 # Complete protocol (concatenated in Step 4)
├── 02_protocol_metadata.json            # Protocol metadata
└── 02_sample_size_calculation.json      # Statistical sample size calculation

Rich Initial Context Support: Users can provide substantial documentation, technical specifications, or research data when initializing the intervention (Step 0). This is preserved in intervention_metadata.json under the initial_context field. Later steps reference this context for more informed protocol development.

Modular Subskill Steps

Each step is an independent skill in references/ directory:

references/
├── 00-initialize-intervention.md    # Collect device or drug information
├── 01-research-protocols.md         # Clinical trials research and FDA guidance
├── 02-protocol-foundation.md        # Protocol sections 1-6 (foundation, design, population)
├── 03-protocol-intervention.md      # Protocol sections 7-8 (intervention details)
├── 04-protocol-operations.md        # Protocol sections 9-12 (assessments, statistics, operations)
└── 05-generate-document.md          # NIH Protocol generation

Utility Scripts

scripts/
└── sample_size_calculator.py   # Statistical power analysis (validated)

Execution Flow

Startup: Welcome and Mode Selection

When skill is invoked, display the following message:

🧬 CLINICAL TRIAL PROTOCOL

Welcome! This skill generates clinical trial protocols for medical devices or drugs.

[If waypoints/intervention_metadata.json exists:]
✓ Found existing protocol in progress: [Intervention Name]
  Type: [Device/Drug]
  Completed: [List of completed steps]
  Next: [Next step to execute]

📋 SELECT MODE:

1. 🔬 Research Only - Run clinical research analysis (Steps 0-1)
   • Collect intervention information
   • Research similar clinical trials
   • Find FDA guidance and regulatory pathways
   • Generate comprehensive research summary as .md artifact

2. 📄 Full Protocol - Generate complete clinical trial protocol (Steps 0-5)
   • Everything in Research Only, plus:
   • Generate all protocol sections
   • Create professional protocol document

3. ❌ Exit

Please select an option (1, 2, or 3):

🛑 STOP and WAIT for user selection (1, 2, or 3)

  • If 1 (Research Only): Set execution_mode = "research_only" and proceed to Research Only Workflow Logic
  • If 2 (Full Protocol): Set execution_mode = "full_protocol" and proceed to Full Workflow Logic
  • If 3 (Exit): Exit gracefully with "No problem! Restart the skill anytime to continue."

Research Only Workflow Logic

This workflow executes only Steps 0 and 1, then generates a formatted research summary artifact.

Step 1: Check for Existing Waypoints

  • If waypoints/intervention_metadata.json exists: Load metadata, check if steps 0 and 1 are already complete
  • If no metadata exists: Start from Step 0

Step 2: Execute Research Steps (0 and 1)

For each step (0, 1):

  1. Check completion status: If step already completed in metadata, skip with "✓ Step [X] already complete"

  2. Execute step:

    • Display "▶ Executing Step [X]..."
    • Read and follow the corresponding subskill file instructions
    • Wait for completion
    • Display "✓ Step [X] complete"
    • Step execution method (ON-DEMAND LOADING): When a step is ready to execute (NOT before), read the subskill markdown file and execute ALL instructions within it
    • Step-to-file mapping:
      • Step 0: references/00-initialize-intervention.md (collect intervention info)
      • Step 1: references/01-research-protocols.md (clinical research and FDA guidance)

  3. Handle errors: If step fails, ask user to retry or exit. Save current state for resume capability.

Step 3: Generate Research Summary Artifact

After Step 1 completes successfully:

  1. Read waypoint files:

    • waypoints/intervention_metadata.json (intervention details)
    • waypoints/01_clinical_research_summary.json (research findings)

  2. Create formatted markdown summary: Generate a comprehensive, well-formatted research summary as a markdown artifact with the following structure:

# Clinical Research Summary: [Intervention Name]

## Intervention Overview

- **Type:** [Device/Drug]
- **Indication:** [Target condition/disease]
- **Description:** [Brief intervention description]
- **Mechanism of Action:** [How it works]

## Similar Clinical Trials

[List top 5-10 similar trials with NCT ID, title, phase, status, key findings]

## FDA Regulatory Pathway

- **Recommended Pathway:** [510(k), PMA, De Novo, IND, NDA, BLA, etc.]
- **Regulatory Basis:** [Rationale for pathway selection]
- **Key Requirements:** [Major regulatory considerations]

## FDA Guidance Documents

[List relevant FDA guidance documents with links and key excerpts]

## Study Design Recommendations

- **Suggested Study Type:** [RCT, single-arm, etc.]
- **Phase Recommendation:** [Phase 1, 2, 3, etc.]
- **Primary Endpoint Suggestions:** [Based on similar trials]
- **Sample Size Considerations:** [Preliminary thoughts]

## Key Insights and Recommendations

[Synthesized recommendations for protocol development]

## Next Steps

[If user wants to proceed with full protocol development]

---
*Generated by Clinical Trial Protocol Skill*
*Date: [Current date]*

  1. Save artifact: Write the formatted summary to waypoints/research_summary.md

  2. Display completion message:

✅ RESEARCH COMPLETE

Research Summary Generated: waypoints/research_summary.md

📊 Key Findings:
  • Similar Trials Found: [X trials]
  • Recommended Pathway: [Pathway name]
  • FDA Guidance Documents: [X documents identified]
  • Study Design: [Recommended design]

📄 The research summary has been saved as a formatted markdown artifact.

Would you like to:
1. Continue with full protocol generation (steps 2-5)
2. Exit and review research summary

Option 1 Logic (Continue to Full Protocol):

  • Set execution_mode = "full_protocol"
  • Continue to Full Workflow Logic starting from Step 2 (since 0 and 1 are complete)

Option 2 Logic (Exit):

  • Display: "✓ Research summary saved. Restart the skill anytime to continue with protocol generation."
  • Exit orchestrator gracefully

Full Workflow Logic

Step 1: Check for Existing Waypoints

  • If waypoints/intervention_metadata.json exists: Load metadata, check completed_steps array, resume from next incomplete step
  • If no metadata exists: Start from Step 0

Step 2: Execute Steps in Order

For each step (0, 1, 2, 3, 4, 5):

  1. Check completion status: If step already completed in metadata, skip with "✓ Step [X] already complete"

  2. Execute step: Display "▶ Executing Step [X]...", read and follow the corresponding subskill file instructions, wait for completion, display "✓ Step [X] complete"

    • Step execution method (ON-DEMAND LOADING): When a step is ready to execute (NOT before), read the subskill markdown file and execute ALL instructions within it
    • IMPORTANT: Do NOT read subskill files in advance. Only read them at the moment of execution.
    • Step-to-file mapping:
      • Step 0: references/00-initialize-intervention.md (read when Step 0 executes)
      • Step 1: references/01-research-protocols.md (read when Step 1 executes)
      • Step 2: references/02-protocol-foundation.md (read when Step 2 executes - sections 1-6)
      • Step 3: references/03-protocol-intervention.md (read when Step 3 executes - sections 7-8)
      • Step 4: references/04-protocol-operations.md (read when Step 4 executes - sections 9-12)
      • Step 5: references/05-concatenate-protocol.md (read when Step 5 executes - final concatenation)

  3. Handle errors: If step fails, ask user to retry or exit. Save current state for resume capability.

  4. Display progress: "Progress: [X/6] steps complete", show estimated remaining time

  5. Step 4 Completion Pause: After Step 4 completes, pause and display the Protocol Completion Menu (see below). Wait for user selection before proceeding.

Step 2.5: Protocol Completion Menu

After Step 4 completes successfully, display the EXACT menu below (do not improvise or create alternative options):

✅ PROTOCOL COMPLETE: Protocol Draft Generated

Protocol Details:
  • Study Design: [Design from metadata]
  • Sample Size: [N subjects from metadata]
  • Primary Endpoint: [Endpoint from metadata]
  • Study Duration: [Duration from metadata]

Protocol file: waypoints/02_protocol_draft.md
File size: [Size in KB]

📋 WHAT WOULD YOU LIKE TO DO NEXT?

1. 📄 Review Protocol in Artifact - click on the .md file above

2. 📄 Concatenate Final Protocol (Step 5)

3. ⏸️  Exit and Review Later

Option 1 Logic (Review in Artifact): Pause, let user open the section files, wait for further instruction

Option 2 Logic (Concatenate Protocol):

  1. Execute Step 5 by reading and following references/05-concatenate-protocol.md
  2. Step 5 will concatenate all section files into final protocol document
  3. Continue to Step 3 (Final Summary) after Step 5 completes

Option 3 Logic (Exit):

  1. Display: "✓ Protocol sections saved. You can resume with Step 5 anytime to concatenate."
  2. Exit orchestrator gracefully

Step 3: Final Summary

Display completion message with:

  • Intervention name, type (device/drug), indication
  • Protocol details (design, sample size, endpoints, duration)
  • All completed steps list
  • Final deliverable: Complete protocol markdown file location (waypoints/protocol_complete.md)
  • Waypoint files list for reference
  • Important disclaimers (FDA Pre-Sub, biostatistician review, IRB approval required)
  • Thank you message

Technical Details

Waypoint File Formats

JSON Waypoints (Steps 0, 1):

  • Structured data for programmatic access
  • Small file sizes (1-15KB)
  • Easy to parse and reference

Markdown Waypoints (Steps 2, 3, 4):

  • Step 2: 02_protocol_foundation.md (Sections 1-6)
  • Step 3: 03_protocol_intervention.md (Sections 7-8)
  • Step 4: 04_protocol_operations.md (Sections 9-12)
  • Step 4: 02_protocol_draft.md (concatenated complete protocol)
  • Human-readable protocol documents
  • Can be directly edited by users
  • Individual section files preserved for easier regeneration

Data Minimization Strategy

Each step implements aggressive summarization:

  • Keep: Top-N results (5-10 max)
  • Keep: Key facts and IDs (NCT numbers, endpoint types)
  • Keep: Concise rationale (2-3 sentences)
  • Discard: Raw MCP query results (not needed after analysis)
  • Discard: Full FDA guidance text (only excerpts/citations kept)
  • Discard: Lower-ranked search results

Step Independence

Each subskill is designed to:

  • Read only from waypoint files (not conversation history)
  • Produce complete output in single execution
  • Not depend on conversation context from previous steps
  • Be runnable standalone

Error Handling

MCP Server Unavailable

  • Detected in: Step 1
  • Action: Display error with installation instructions
  • Allow user to retry after installing MCP server
  • No fallback available - MCP server is required for protocol research

Step Fails or Returns Error

  • Action: Display error message from subskill
  • Ask user: "Retry step? (Yes/No)"
    • Yes: Re-run step
    • No: Save current state, exit orchestrator

User Interruption

  • All progress saved in waypoint files
  • User can resume anytime by restarting the skill
  • Workflow automatically detects completed steps and resumes from next step
  • No data loss

Disclaimers

⚠️ IMPORTANT: This protocol generation tool provides preliminary clinical study protocol based on NIH/FDA guidelines and similar trials. It does NOT constitute:

  • Official FDA or IRB determination or approval
  • Medical, legal, or regulatory advice
  • Substitute for professional biostatistician review
  • Substitute for FDA Pre-Submission meeting
  • Guarantee of regulatory or clinical success

REQUIRED before proceeding with clinical study:

  • Biostatistician review and sample size validation
  • FDA Pre-Submission meeting (Q-Submission for devices, Pre-IND for drugs)
  • IRB review and approval
  • Clinical expert and regulatory consultant engagement
  • Legal review of protocol and informed consent
  • Site investigator review and input
  • Sponsor completion of all [TBD] items in protocol

PROFESSIONAL CONSULTATION STRONGLY RECOMMENDED

Clinical trial protocols are complex, high-stakes documents requiring expertise across multiple disciplines. Professional consultation with clinical trial experts, biostatisticians, and regulatory affairs specialists is essential before proceeding with clinical study planning.