Scientific Manuscript Writer

Orchestrates the creation of scientific manuscript drafts through a structured, note-generating workflow.

Core Principle: No Silent Assumptions

This skill NEVER makes assumptions about user data without explicit confirmation.

When encountering ambiguity in data, code, or figures:

1. STOP and ask the user for clarification
2. DOCUMENT all clarifications received
3. VERIFY interpretations before drafting

It is better to ask too many questions than to misinterpret the user’s research. Every clarification is logged in the relevant notes files for transparency.

Specialist Agents

This skill employs specialist agents for domain expertise:

Statistical Reviewer Agent

The statistical reviewer (agents/statistical-reviewer.md) ensures:

• Appropriate statistical test selection
• Assumption checking and validation
• Correct statistical reporting format
• Effect sizes with confidence intervals
• Multiple comparison handling

No statistical claims are published without statistical reviewer sign-off.

Academic Reviewer Agent

The academic reviewer (agents/academic-reviewer.md) acts as a skeptical peer reviewer:

• Verifies every claim is supported by its cited reference
• Validates the hypothesis is scientifically meaningful and testable
• Confirms methods actually test the stated hypothesis
• Independently interprets results before reading Discussion
• Identifies discrepancies between evidence and author conclusions
• Flags overstatements and unsupported claims
• Routes issues to other agents or user for resolution

No manuscript proceeds to final assembly without academic reviewer approval.

Expected Project Structure

User must organize their project folder as follows:

project/
├── papers/              # PDF files of relevant literature
│   ├── smith-2023.pdf
│   ├── jones-2022.pdf
│   └── ...
├── data/                # Raw data outputs (CSV, Excel)
│   ├── results.csv
│   ├── demographics.csv
│   └── ...
├── figures/             # Generated figures (PNG, JPG, SVG)
│   ├── figure1.png
│   ├── figure2.png
│   └── ...
├── ethics/              # OPTIONAL - Ethics/governance documents (.pdf, .docx, .md)
│   ├── protocol.pdf     # Approved protocol (IRB, IACUC, ethics committee, etc.)
│   └── amendments/      # Optional protocol amendments
└── config.md            # Project configuration (see template below)

Ethics Documents (Optional)

If provided, ethics/governance documents enable:

• Auto-populated ethics statement in final manuscript
• Scope comparison checkpoint during scoping (catches discrepancies early)
• Cross-reference validation in Methods and Results (ensures consistency)

Supports: IRB protocols, IACUC approvals, ethics committee decisions, data governance agreements.

Supported formats: PDF, Word (.docx), Markdown (.md)

config.md Template

# Project Configuration

## GitHub Repository
url: https://github.com/username/repo-name
branch: main
access: private  # or public

## Constraints
word_limit: 3500
target_journal: [Target Journal]
citation_style: AMA

## Additional Notes
[Any other context for the manuscript]

Output Structure

The skill generates intermediate notes and drafts:

project/
├── notes/
│   ├── papers/              # Condensed notes per PDF (via subagent)
│   │   ├── smith-2023.md
│   │   └── jones-2022.md
│   ├── papers-library/      # ALL PDFs stored centrally
│   │   ├── smith-2023.pdf
│   │   └── jones-2022.pdf
│   ├── bibliography.md      # Master bibliography with citations/links
│   ├── literature-synthesis.md  # Aggregated themes and findings
│   ├── code-analysis.md     # GitHub repo analysis
│   ├── data-analysis.md     # Data/figures interpretation
│   ├── ethics-summary.md       # Ethics document extraction (if ethics/ provided)
│   ├── ethics-scope-comparison.md  # Ethics vs actual scope (if ethics/ provided)
│   ├── statistical-review.md    # Statistical reviewer sign-off report
│   └── reviewer-feedback.md     # Academic reviewer feedback
├── drafts/
│   ├── introduction.md
│   ├── methods.md
│   ├── results.md
│   ├── discussion.md
│   └── abstract.md
├── inventory.md             # What's available in project
├── scope.md                 # Research question, findings, constraints
└── manuscript.md            # Final assembled draft

Workflow

[1. Context Ingestion] ─── skills/context-ingestion/SKILL.md
│   - Scan project folder structure
│   - Validate required folders exist
│   - Clone/analyze GitHub repository
│   - Extract ethics content → notes/ethics-summary.md (if ethics/ exists)
│   - Generate inventory.md
│
▼
[2. Scoping] ─── skills/scoping/SKILL.md
│   - Ask: research question
│   - Ask: key findings (cross-check with inventory)
│   - Ask: constraints (word limit, journal)
│   - ★ ETHICS SCOPE COMPARISON → Confirm discrepancies with user (if ethics docs exist)
│   - Generate scope.md, notes/ethics-scope-comparison.md
│
▼
[3. Literature Review] ─── skills/literature-review/SKILL.md
│   - ★ SUBAGENT PER PAPER → Prevents context overflow
│   - Process each PDF via isolated subagent → notes/papers/*.md
│   - Synthesize from condensed notes → notes/literature-synthesis.md
│   - Draft Introduction → drafts/introduction.md
│
▼
[4. Code Analysis] ─── skills/code-analyzer/SKILL.md
│   - Analyze GitHub repository
│   - Extract methodology → notes/code-analysis.md
│   - ★ STATISTICAL REVIEW → Validate methods
│   - Draft Methods → drafts/methods.md
│
▼
[5. Results Interpretation] ─── skills/results-interpreter/SKILL.md
│   - Analyze CSV data files
│   - Interpret figures
│   - Generate → notes/data-analysis.md
│   - ★ STATISTICAL REVIEW → Validate statistics
│   - Draft Results → drafts/results.md
│
▼
[6. Synthesis] ─── skills/synthesis/SKILL.md
│   - Read all notes/*.md
│   - Read drafts/introduction.md, methods.md, results.md
│   - Draft Discussion → drafts/discussion.md
│   - Draft Abstract → drafts/abstract.md
│
▼
[7. Academic Review] ─── agents/academic-reviewer.md
│   - Verify claims against citations
│   - Validate hypothesis and methods alignment
│   - ★ INDEPENDENTLY interpret results
│   - Compare to Discussion conclusions
│   - Generate → notes/reviewer-feedback.md
│   - Route issues to agents or user
│
▼
[8. Assembly] ─── skills/assembler/SKILL.md
    - Confirm reviewer approval
    - Combine all drafts
    - Populate ethics statement from ethics docs (if available)
    - Apply formatting constraints
    - Generate → manuscript.md

Entry Points

The workflow supports multiple entry points:

Executing the Workflow

Step 1: Context Ingestion

Read skills/context-ingestion/SKILL.md and follow it to:

• Validate project folder structure
• Parse config.md for GitHub URL and constraints
• Clone or fetch GitHub repository
• Inventory all available materials
• Output: inventory.md

Step 2: Scoping

Read skills/scoping/SKILL.md and follow it to:

• Review inventory.md
• Ask user for research question
• Ask user for key findings (validate against data)
• Confirm constraints from config.md
• Output: scope.md

Step 3: Literature Review

Read skills/literature-review/SKILL.md and follow it to:

• Process user-provided PDFs in papers/ via isolated subagents → notes/papers/*.md
• Save PDFs to central library → notes/papers-library/*.pdf
• Generate bibliography with citations → notes/bibliography.md
• Synthesize findings → notes/literature-synthesis.md
• Draft Introduction → drafts/introduction.md

Step 4: Code Analysis

Read skills/code-analyzer/SKILL.md and follow it to:

• Analyze cloned GitHub repository
• Extract methodology, statistical approaches, tools
• Output: notes/code-analysis.md, drafts/methods.md

Step 5: Results Interpretation

Read skills/results-interpreter/SKILL.md and follow it to:

• Analyze CSV files in data/
• Interpret figures in figures/
• Output: notes/data-analysis.md, drafts/results.md

Step 6: Synthesis

Read skills/synthesis/SKILL.md and follow it to:

• Read all accumulated notes
• Integrate findings with literature context
• Output: drafts/discussion.md, drafts/abstract.md

Step 7: Assembly

Read skills/assembler/SKILL.md and follow it to:

• Combine all draft sections
• Apply word limit and formatting
• Generate reference list
• Output: manuscript.md

References

• references/section-guidelines.md – Writing conventions per section
• references/citation-format.md – Citation formatting styles
• references/source-note-template.md – Template for paper notes