Mac

# Create scientific-analysis-architect skill

**Date**: 2026-02-04
**Machine**: mac
**Status**: Complete

## Objective

Create a new multi-agent skill for planning scientific research analyses using Jupyter notebooks with pseudocode. The skill orchestrates 11 agents across 6 phases, is biology-agnostic (agents request context, never inject), includes interview-mode statistical fact-checking, and supports session persistence for resume capability.

## Changes Planned

- [x] Follow CONFIG_MANAGEMENT.md workflow
- [x] Create SKILL.md with 6-phase workflow overview
- [x] Create references/agent-definitions.md (11 agents)
- [x] Create references/phase-workflows.md (detailed workflows)
- [x] Create references/session-schema.md (JSON schema)
- [x] Create references/error-handling.md (compensation actions, circuit breakers)
- [x] Create references/interview-protocol.md (Phase 6 interview)
- [x] Create references/notebook-templates.md (pseudocode levels)
- [x] Create references/quality-gates.md (gate definitions)
- [x] Create examples/rnaseq-analysis-plan.md (full walkthrough)
- [x] Create examples/statistical-interview-session.md (interview scenarios)

## Expected Outcome

A fully functional skill that:
- Completes 6-phase workflow for multi-chapter analysis (56-76 min)
- Outputs valid .ipynb files with pseudocode
- Maintains biology-agnostic design
- Supports session resume from any phase
- Includes comprehensive error handling

## Actual Outcome

All 10 files created and synced to ~/.claude/ successfully:

**Files created**:
- `claude-config/skills/scientific-analysis-architect/SKILL.md` (11,564 bytes)
- `claude-config/skills/scientific-analysis-architect/references/agent-definitions.md` (10,786 bytes)
- `claude-config/skills/scientific-analysis-architect/references/phase-workflows.md` (14,420 bytes)
- `claude-config/skills/scientific-analysis-architect/references/session-schema.md` (15,281 bytes)
- `claude-config/skills/scientific-analysis-architect/references/error-handling.md` (11,080 bytes)
- `claude-config/skills/scientific-analysis-architect/references/interview-protocol.md` (11,137 bytes)
- `claude-config/skills/scientific-analysis-architect/references/notebook-templates.md` (12,686 bytes)
- `claude-config/skills/scientific-analysis-architect/references/quality-gates.md` (12,258 bytes)
- `claude-config/skills/scientific-analysis-architect/examples/rnaseq-analysis-plan.md` (14,837 bytes)
- `claude-config/skills/scientific-analysis-architect/examples/statistical-interview-session.md` (10,659 bytes)

**Total**: ~114KB across 10 files

## Assessment

**Result**: Success

**Improvements**:
- New skill available for scientific analysis planning
- Comprehensive error handling with consolidated escalation
- Session persistence enables resume from interruptions
- Interview mode prevents tedium with batch options

**Issues**:
- None identified during implementation

**Lessons Learned**:
- Detailed implementation plan from Phase 3 (decision-synthesizer) made execution straightforward
- Pre-implementation safety checks (git status, sync-config status) caught no issues
- YAML validation before writing prevents syntax errors

## Related Commits

- [Pending]: feat(scientific-analysis-architect): Create multi-agent scientific analysis planning skill

## Next Steps

- Commit changes (2 atomic commits: core + examples)
- Test skill invocation in real scenario
- Consider adding optional handoff to programming-pm for implementation