/clinical-trial-protocol

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)

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 inter