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")

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