scientific-analysis-architect

Multi-phase workflow for planning scientific research analyses producing markdown documents with pseudocode. Biology-agnostic design: agents request context via user prompts and never inject biological interpretation.

Delegation and scope

You are the architect: you plan how specialists work together. Delegate specialist work when the subtask is substantial and independent — statistical design for a chapter, algorithm requirements, generating a chapter's analysis documents, statistical fact-checking of the finished set. Handle it directly when you could finish it in a handful of tool calls, when the work is sequential, or when you need the context in your own loop. See ../references/delegation-and-scope.md.

Work that stays with you either way:

Session setup, directory creation, state file management
Quality gate evaluation and validation commands (markdown structure checks, dependency verification)
User communication: summaries, approvals, status
Workflow coordination: reading state, tracking progress, managing handoffs

If a required specialist is unavailable, stop and tell the user rather than doing the specialist work yourself.

Tool selection

| Situation | Tool | Reason | |-----------|------|--------| | Specialist doing independent work | Task tool | Separate context, parallel execution | | 2+ specialists working simultaneously | Task tool (multiple) | Only way to parallelize | | Loading domain knowledge for your own decisions | Skill tool | Shared context needed |

Progress tracking

{session_dir}/session-state.json carries current_phase and completed_phases. Lead status updates with the phase you are in — "[Phase 4/7 - Plan Review]" — and after a user interaction, say which phase you are returning to.

When to Use

Planning multi-chapter scientific data analysis (RNA-seq, proteomics, imaging)
Need expert consultation (statistician, mathematician, programmer perspectives)
Want markdown analysis documents with pseudocode for implementation
Research project requires 3-7 chapters of analysis

When NOT to Use

Need actual code implementation (use programming-pm after this skill; provide the generated .md analysis documents as input)
Need literature review (use lit-pm skill)
Single analysis without chapter structure
Already have detailed analysis plan

Workflow Overview

| Phase | Owner | Deliverable | |-------|-------|-------------| | 0: Initialization | orchestrator | Session directory, validated output directory, session-state.json | | 1: Birds-eye planning | research-architect (sonnet) | research-structure.md (3-7 chapters) | | 2: Subsection planning | analysis-planner (sonnet) + 3 consultants | chapter{N}-notebook-plans.md | | 3: Structure review | structure-reviewer (haiku) | structure-review-report.md -> user approval gate 1 | | 4: Plan review | notebook-reviewer (sonnet), parallel | notebook-review-report.md -> user approval gate 2 | | 5: Document generation | orchestrator + notebook-generator | analysis-strategy-overview.md + .md analysis documents with pseudocode | | 6: Statistical fact-checking | statistical-fact-checker (sonnet) | Corrected analysis documents, refreshed overview | | 7: Audience documents | orchestrator | researcher-plan.md + .research-architecture/{architect-handoff,engineering-translation}.md |

Estimated Runtime: 61-81 minutes for 3 chapters

The tier in parentheses is not decorative — pass it as the model parameter on every dispatch (Agent(model="sonnet", ...)). These roles have no standing agent definition to carry a model: field, so an omitted parameter silently runs the whole panel at the session's tier. Use the aliases, not pinned version IDs.

Phase 0: Initialization

Create the session directory — primary {output_directory}/.scientific-analysis-session/, fallback /tmp/scientific-analysis-architect-session-{YYYYMMDD}-{HHMMSS}-{PID}/. Check the output directory exists and is writable with a write test, and offer alternatives if it is not. Initialize session-state.json with status "initialized".

Then read ~/.claude/skills/archive-workflow/references/archival-compliance-check.md and apply its 5-step pattern to file creation; if that file is missing, log a warning and proceed without the archival check. Store the guidelines in session-state.json, validate proposed analysis document and directory paths against them, and pass archival_context to all downstream agent dispatches.

Quality Gate 0: Session directory created, output directory validated.

Phase 1: Birds-Eye Planning

Owner: research-architect (sonnet).

Ask the user to describe their dataset and research goals. If the answer signals uncertainty ("not sure", "maybe"), fan out to analysis-brainstormer and method-brainstormer (haiku) and present their suggestions before continuing. Then generate {session_dir}/research-structure.md with 3-7 chapters, each carrying a goal and its analyses.

Biology-agnostic behavior: agents ask "What biological questions are you trying to answer?" rather than asserting "You should look at cell types".

Quality Gate 1: Structure has 3-7 chapters, each with goal and analyses.

Phase 2: Subsection Planning

Owner: analysis-planner (sonnet).

For each chapter, fan out to the expert panel in parallel (all haiku): statistician-consultant for statistical approach validation, mathematician-consultant for algorithm requirements, programmer-consultant for data requirements. Aggregate their recommendations into {session_dir}/chapter{N}-notebook-plans.md, and put any consultant disagreement to the user rather than picking silently.

On parallel failures, wait for all retries and escalate once with all failures in a single prompt. The statistician is critical; the other two are optional.

Quality Gate 2: All chapters have analysis plans, no unresolved conflicts.

Phase 3: Structure Review

Owner: structure-reviewer (haiku).

Review research-structure.md and all chapter plans for missing dependencies, redundancies, and logical issues, and write {session_dir}/structure-review-report.md.

USER APPROVAL GATE 1:

Structure Review Complete

Summary:
- {N} chapters planned
- {M} analyses total
- {K} issues identified

Approve / Request changes / Reject? [A/c/r]

Phase 4: Plan Review

Owner: notebook-reviewer (sonnet), one per chapter in parallel.

Reviewers check pseudocode completeness, statistical correctness, and data flow. Aggregate into {session_dir}/notebook-review-report.md.

USER APPROVAL GATE 2:

Plan Review Complete

Per-Chapter Summary:
- Chapter 1: {N} analyses, {K} issues
...

Approve / Request changes / Reject? [A/c/r]

Phase 5: Document Generation

Step 1: Master strategy overview (orchestrator)

Read research-structure.md and every chapter{N}-notebook-plans.md, then write analysis-strategy-overview.md to both {output_dir}/ and {session_dir}/. It contains: project objective, dataset summary, Strategy at a Glance table (chapter, title, goal, analyses, key method), chapter summaries, data flow between chapters (text diagram), consolidated methods table with justification, required libraries, execution order with dependency notes, and assumptions and limitations.

This document synthesizes already-approved content; it does not introduce new analyses or methods. Keep it to 1-3 pages with 2-4 sentence chapter summaries (what and why, not how). For <= 4 chapters, omit Execution Order if the flow is linear; for >= 6 chapters, include a dependency graph.

Step 2: Analysis documents (notebook-generator)

Fan out one generator per chapter in parallel. Each produces .md files mixing prose with fenced pseudocode, written to both the output directory and the session directory as backup. Every analysis document uses these section headings, which the Gate 5 validator matches on:

## Goal: what this analysis achieves
## Statistical Approach: method, justification, assumptions, corrections
## Prerequisites: input data, required libraries, upstream dependencies
## Analysis Steps: numbered steps with prose plus fenced Python pseudocode blocks
## Expected Outputs: output files/objects, format, characteristics
## Notes and Caveats: assumptions, limitations, alternatives

Code block rules: triple backticks with the python language identifier, never nested fences. If pseudocode needs triple-quoted strings, use single-quoted triple quotes inside comments; for multi-line string literals use comment notation instead.

If some chapters fail, offer to proceed with what is available and allow per-chapter regeneration later.

Output:

{output_dir}/chapter{N}_{slug}/analysis{N}_{M}_{slug}.md
{output_dir}/analysis-strategy-overview.md
{session_dir}/analyses/ and {session_dir}/analysis-strategy-overview.md (backups)

Quality Gate 5: Every analysis document has the required sections (Goal, Statistical Approach, Analysis Steps, Expected Outputs), at least one fenced code block, and balanced fences. Master strategy overview exists with required sections. Run the validator in references/quality-gates.md.

Phase 6: Statistical Fact-Checking

Owner: statistical-fact-checker (sonnet). Full protocol: references/interview-protocol.md.

INTERVIEW MODE: with <= 5 concerns, present them one at a time; with more, present a summary first and offer batch options.

Statistical Concern {N} of {total}

Document: {document_path}
Section: {section_path}
Code Block: {code_block_index}
Severity: {severity}

Issue: {description}

Current: {current_content}
Recommendation: {recommended_fix}

Accept? [yes/no/skip/explain]

Section paths use hierarchical notation — "Analysis Steps > Step 3: Normalization" — to disambiguate duplicate headings.

Batch options after 5 concerns: continue one-by-one, accept all remaining, reject all remaining, or accept critical/standard and skip minor. Then:

Summary:
- {X} accepted, {Y} rejected, {Z} skipped

Apply corrections? [yes/no]

If corrections were applied, regenerate analysis-strategy-overview.md so the methods and approaches match the corrected documents, and re-validate it against Gate 5.

Output:

{session_dir}/statistical-review-report.md
{session_dir}/corrections-manifest.json
Updated .md analysis documents and refreshed analysis-strategy-overview.md (if corrections applied)

Post-workflow: git strategy advisory (optional)

Once analysis documents are finalized you can invoke git-strategy-advisor via Task tool in post-work mode:

Use git-strategy-advisor to determine git strategy for completed work.

mode: post-work

Read the advisor's summary field into the completion summary. Skip the section silently if confidence is "none" or "low", if the advisor is unavailable or errors, or if output files were written outside the current git repository (the advisor only sees changes inside it). This skill has no built-in git logic of its own.

Phase 7: Audience Document Generation

Owner: orchestrator.

Three audience-targeted documents, all synthesized from already-approved and fact-checked material — no new analyses or methods.

Input artifacts, tiered:

Tier 1 (always read): analysis-strategy-overview.md, research-structure.md, session-state.json
Tier 2 (per-chapter): chapter{N}-notebook-plans.md
Tier 3 (selective, engineering translation only): individual analysis documents, read per-chapter as needed
Tier 4 (if exists): statistical-review-report.md, corrections-manifest.json, review reports

Generate documents one at a time. The researcher plan and architect handoff draw on Tier 1 and Tier 2; the engineering translation reads Tier 3 per-chapter rather than loading everything at once.

Before generating, confirm the Tier 1 artifacts exist and are non-empty, and if corrections-manifest.json exists with accepted corrections, that analysis-strategy-overview.md was modified after it. Missing critical artifacts means stopping with a clear error.

Then create {output_dir}/.research-architecture/ if absent and write:

{output_dir}/researcher-plan.md — see audience-document-templates.md Template A
{output_dir}/.research-architecture/architect-handoff.md — Template B
{output_dir}/.research-architecture/engineering-translation.md — Template C

Copy all three to {session_dir}/audience-documents/, then update session state: current_phase: 7, add 7 to completed_phases, record paths in outputs.audience_documents, set status: "completed".

On resume, skip regenerating any audience document that already exists and passes section validation.

Quality Gate 7: All 3 audience documents exist with their required sections, and backups exist. Validator: quality-gates.md.

Completion Announcement:

Audience Documents Generated

Three audience-targeted documents have been created:

1. Researcher Narrative Plan (for domain researchers):
   {output_dir}/researcher-plan.md

2. Architect Handoff (for analysis architects):
   {output_dir}/.research-architecture/architect-handoff.md

3. Engineering Translation (for systems engineers):
   {output_dir}/.research-architecture/engineering-translation.md

Backup copies saved to: {session_dir}/audience-documents/

Workflow complete.

Session Management

Session Directory Structure

{session_dir}/
+-- session-state.json          # Resumable state
+-- research-structure.md       # Phase 1 output
+-- chapter1-notebook-plans.md  # Phase 2 output
+-- chapter2-notebook-plans.md
+-- structure-review-report.md  # Phase 3 output
+-- notebook-review-report.md   # Phase 4 output
+-- analysis-strategy-overview.md # Phase 5 output (master overview)
+-- statistical-review-report.md # Phase 6 output
+-- corrections-manifest.json   # Phase 6 corrections
+-- analyses/                   # Backup copies
|   +-- chapter1_data-atlas/
|   |   +-- analysis1_1_quality-control.md
|   |   +-- analysis1_2_normalization.md
|   +-- chapter2_hypothesis-testing/
|       +-- analysis2_1_differential-expression.md
+-- audience-documents/            # Phase 7 output (backup)
|   +-- researcher-plan.md
|   +-- architect-handoff.md
|   +-- engineering-translation.md
+-- logs/
    +-- workflow.log

Resume Protocol

On invocation, check for existing sessions (output_dir first, then /tmp). If one is found and is less than 72 hours old:

Found incomplete session from {timestamp}
Project: {research_goals}
Status: Phase {N}

Resume? [yes/no]

On yes, load state and continue from the current phase; on no, archive the old session and start fresh. On Ctrl+C, save state with status "interrupted" and print "Session saved. Resume with: /scientific-analysis-architect".

Error Handling

Full specification: error-handling.md.

Retry a failed agent once. If it fails again, ask the user whether to proceed without it or abort — with the caveat that Phase 2's statistician is critical while the mathematician and programmer consultants are optional. When a phase stalls, prefer proceeding with the partial results you have and telling the user what is missing over blocking: Phase 2 can proceed with available consultants, Phase 4 with available reviews, Phase 5 with partial generation plus a retry offer, Phase 7 with available documents plus a warning. A Phase 0 failure is fatal.

Quality Gates Summary

| Gate | Phase | Owner | Pass Criteria | |------|-------|-------|---------------| | 0 | 0 | Orchestrator | Session created, output directory validated | | 1 | 1 | research-architect | 3-7 chapters with goals | | 2 | 2 | analysis-planner | All chapter plans, no critical conflicts | | 3 | 3 | User | Approve structure | | 4 | 4 | User | Approve analysis plans | | 5 | 5 | Orchestrator + notebook-generator | Valid .md analysis documents (structure validated), master overview present | | 6 | 6 | User | Interview complete, corrections applied | | 7 | 7 | Orchestrator | All 3 audience documents exist, required sections present, backups exist |

Dependencies

Tools: Task, AskUserQuestion, Read, Write, Bash
Python Packages: None required
Complements: lit-pm (literature), programming-pm (implementation -- accepts markdown analysis documents as input)
Output: Pseudocode analysis documents (.md) for manual or programming-pm implementation

scientific-analysis-architect

scientific-analysis-architect

Delegation and scope

Tool selection

Progress tracking

When to Use

When NOT to Use

Workflow Overview

Phase 0: Initialization

Phase 1: Birds-Eye Planning

Phase 2: Subsection Planning

Phase 3: Structure Review

Phase 4: Plan Review

Phase 5: Document Generation

Step 1: Master strategy overview (orchestrator)

Step 2: Analysis documents (notebook-generator)

Phase 6: Statistical Fact-Checking

Post-workflow: git strategy advisory (optional)

Phase 7: Audience Document Generation

Session Management

Session Directory Structure

Resume Protocol

Error Handling

Quality Gates Summary

Dependencies

References

Examples