Clinical Trial Protocol Implementation Requirements

Implementation Requirements

Implementation Requirements

When this skill is invoked:

1. Display the welcome message with mode selection (shown in "Startup: Welcome and Mode Selection" section)

2. Wait for user mode selection (1: Research Only, 2: Full Protocol, 3: Exit)

3. Execute based on selected mode:

   • Research Only Mode (Option 1):
     • Execute Research Only Workflow Logic (Steps 0-1 only)
     • Generate formatted research summary as .md artifact
     • Offer option to continue with full protocol or exit
   • Full Protocol Mode (Option 2):
     • Execute Full Workflow Logic (Steps 0-5)
     • Check for existing waypoints and resume from last completed step
     • OR start from Step 0 if no waypoints exist
     • Execute all steps sequentially until complete

4. For each step execution (LAZY LOADING - On-Demand Only):

   • ONLY when a step is ready to execute, read the corresponding subskill file
   • Do NOT read subskill files in advance or "to prepare"
   • Example: When Step 1 needs to run, THEN read references/01-research-protocols.md and follow its instructions
   • For protocol development: Execute Steps 2, 3, 4 sequentially in order
   • Do NOT try to execute multiple steps in parallel - run sequentially
   • Read each step's subskill file only when that specific step is about to execute

5. Research summary artifact generation (Research Only Mode):

   • After Step 1 completes, read waypoint files
   • Generate comprehensive, well-formatted markdown summary
   • Save to waypoints/research_summary.md
   • Display completion message with key findings

6. Handle errors gracefully:

   • If a step fails, give user option to retry or exit
   • If MCP server unavailable, explain how to install
   • All progress is saved automatically in waypoints

7. Track progress:

   • Update waypoints/intervention_metadata.json after each step
   • Show progress indicators to user (e.g., "Progress: 3/6 steps complete" or "Progress: 2/2 research steps complete")
   • Provide clear feedback on what's happening

8. Final output:

   • Research Only: Display research summary location and offer to continue with full protocol
   • Full Protocol: Congratulate user, display protocol location and next steps
   • Remind user of disclaimers