Clinical Trial Protocol Waypoint Based Design

Waypoint-Based Design (+2)

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)