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From bio-research
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.
npx claudepluginhub fergupa/claude_plugins --plugin bio-researchHow this skill is triggered — by the user, by Claude, or both
Slash command
/bio-research:clinical-trial-protocolThe summary Claude sees in its skill listing — used to decide when to auto-load this skill
**CRITICAL: This orchestrator follows a SIMPLE START approach:**
LICENSE.txtassets/FDA-Clinical-Protocol-Template.mdreferences/00-initialize-intervention.mdreferences/01-research-protocols.mdreferences/02-protocol-foundation.mdreferences/03-protocol-intervention.mdreferences/04-protocol-operations.mdreferences/05-concatenate-protocol.mdscripts/sample_size_calculator.pyAssesses clinical trial feasibility across 6 dimensions using precedent trials and FDA guidance. Produces enrollment projections, endpoint recommendations, and regulatory pathway analysis.
Guides clinical and health science research through PICOT question formulation, evidence hierarchy assessment, bias evaluation (Cochrane RoB 2, ROBINS-I), outcome prioritization, and GRADE certainty rating.
Generates clinical decision support documents for pharmaceutical research: biomarker-stratified cohort analyses with survival statistics, GRADE-graded treatment recommendations, and publication-ready LaTeX/PDF output.
Share bugs, ideas, or general feedback.
CRITICAL: This orchestrator follows a SIMPLE START approach:
Why this matters:
This skill generates clinical trial protocols for medical devices or drugs using a modular, waypoint-based architecture
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
📄 Full Protocol Mode (Steps 0-5): 0. Initialize Intervention - Collect device or drug information
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.
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
scripts/
└── sample_size_calculator.py # Statistical power analysis (validated)
Installation:
.mcpb file into Claude DesktopAvailable Tools:
search_clinical_trials - Search by:
condition - Disease or condition (e.g., "pancreatic cancer") intervention - Drug, device, or treatment (e.g., "pembrolizumab", "CAR-T") sponsor - Sponsor or collaborator name (e.g., "Pfizer", "NIH") location - City, state, or country (e.g., "California", "Boston") status - "recruiting" (default), "active", "completed", "all" phase - Trial phase: "1", "2", "3", "4", "early_phase1" max_results - Default 25, max 100
get_trial_details - Get comprehensive details for a specific trial using its nct_id (e.g., "NCT04267848"). Returns eligibility criteria, outcomes, study design, and contact information.
Verification: Step 1 will automatically test MCP connectivity at startup.
Purpose: FDA regulatory pathway research via explicit database URLs
Sources:
Template Files: Any .md files in the assets/ directory
Purpose: Reference template for protocol structure and content guidance. The system automatically detects available templates and uses them dynamically.
Installation:
pip install -r requirements.txt
Dependencies:
Purpose: Accurate statistical sample size calculations for clinical protocols
Simply invoke the skill and select your desired mode:
🔬 Research Only Mode:
📄 Full Protocol Mode:
Resume Capability: If interrupted, simply restart the skill and it will automatically resume from your last completed step.
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)
execution_mode = "research_only" and proceed to Research Only Workflow Logicexecution_mode = "full_protocol" and proceed to Full Workflow LogicThis workflow executes only Steps 0 and 1, then generates a formatted research summary artifact.
Step 1: Check for Existing Waypoints
waypoints/intervention_metadata.json exists: Load metadata, check if steps 0 and 1 are already completeStep 2: Execute Research Steps (0 and 1)
For each step (0, 1):
Check completion status: If step already completed in metadata, skip with "✓ Step [X] already complete"
Execute step:
references/00-initialize-intervention.md (collect intervention info)references/01-research-protocols.md (clinical research and FDA guidance)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:
Read waypoint files:
waypoints/intervention_metadata.json (intervention details)waypoints/01_clinical_research_summary.json (research findings)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]*
Save artifact: Write the formatted summary to waypoints/research_summary.md
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):
execution_mode = "full_protocol"Option 2 Logic (Exit):
Step 1: Check for Existing Waypoints
waypoints/intervention_metadata.json exists: Load metadata, check completed_steps array, resume from next incomplete stepStep 2: Execute Steps in Order
For each step (0, 1, 2, 3, 4, 5):
Check completion status: If step already completed in metadata, skip with "✓ Step [X] already complete"
Execute step: Display "▶ Executing Step [X]...", read and follow the corresponding subskill file instructions, wait for completion, display "✓ Step [X] complete"
references/00-initialize-intervention.md (read when Step 0 executes)references/01-research-protocols.md (read when Step 1 executes)references/02-protocol-foundation.md (read when Step 2 executes - sections 1-6)references/03-protocol-intervention.md (read when Step 3 executes - sections 7-8)references/04-protocol-operations.md (read when Step 4 executes - sections 9-12)references/05-concatenate-protocol.md (read when Step 5 executes - final concatenation)Handle errors: If step fails, ask user to retry or exit. Save current state for resume capability.
Display progress: "Progress: [X/6] steps complete", show estimated remaining time
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):
references/05-concatenate-protocol.mdOption 3 Logic (Exit):
Step 3: Final Summary
Display completion message with:
JSON Waypoints (Steps 0, 1):
Markdown Waypoints (Steps 2, 3, 4):
02_protocol_foundation.md (Sections 1-6)03_protocol_intervention.md (Sections 7-8)04_protocol_operations.md (Sections 9-12)02_protocol_draft.md (concatenated complete protocol)Each step implements aggressive summarization:
Each subskill is designed to:
⚠️ IMPORTANT: This protocol generation tool provides preliminary clinical study protocol based on NIH/FDA guidelines and similar trials. It does NOT constitute:
REQUIRED before proceeding with clinical study:
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.
When this skill is invoked:
Display the welcome message with mode selection (shown in "Startup: Welcome and Mode Selection" section)
Wait for user mode selection (1: Research Only, 2: Full Protocol, 3: Exit)
Execute based on selected mode:
For each step execution (LAZY LOADING - On-Demand Only):
references/01-research-protocols.md and follow its instructionsResearch summary artifact generation (Research Only Mode):
waypoints/research_summary.mdHandle errors gracefully:
Track progress:
waypoints/intervention_metadata.json after each stepFinal output: