clinical-trial-protocol-skill

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---
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.