Clinical Trial Protocol Skill

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):

1. Initialize Intervention - Collect device or drug information
2. 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):

1. Initialize Intervention - Collect device or drug information
2. Research Similar Protocols - Find similar trials, FDA guidance, and published protocols
3. Protocol Foundation - Generate protocol sections 1-6 (foundation, design, population)
4. Protocol Intervention - Generate protocol sections 7-8 (intervention details)
5. Protocol Operations - Generate protocol sections 9-12 (assessments, statistics, operations)
6. 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)

Prerequisites

1. clinical trials MCP Server (Required)

Installation:

• Install via drag-and-drop .mcpb file into Claude Desktop
• Or configure manually in Claude Desktop settings

Available 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.

2. FDA Database Access (Built-in)

Purpose: FDA regulatory pathway research via explicit database URLs

Sources:

• Step 1: FDA device/drug databases (510(k), PMA, De Novo, Drugs@FDA, Orange Book, Purple Book)
• All sources use direct FDA database URLs - no generic web searches

3. Clinical Protocol Template

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.

4. Python Dependencies (Required for Step 2)

Installation:

pip install -r requirements.txt

Dependencies:

• scipy >= 1.11.0 (statistical calculations)
• numpy >= 1.24.0 (numerical operations)

Purpose: Accurate statistical sample size calculations for clinical protocols

How to Use

Simply invoke the skill and select your desired mode:

🔬 Research Only Mode:

1. Select "Research Only" from the main menu
2. Provide intervention information
3. Receive comprehensive research summary as formatted .md artifact
4. Option to continue with full protocol generation or exit

📄 Full Protocol Mode:

1. Select "Full Protocol" from the main menu
2. Guide you through all steps sequentially (Steps 0-5)
3. Pause after Step 4 to review the draft protocol
4. Generate the final protocol document when ready

Resume Capability: If interrupted, simply restart the skill and it will automatically resume from your last completed step.

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"

1. Execute step: