Manuscript Planning Protocol

Phase 1: Repository Reconnaissance

1. •Map Structure: Execute tree -L 2 --prune to understand the project layout.
2. •Locate Assets:
   • •Find all data files (*.csv, *.xlsx) in data/.
   • •Find all analysis notebooks (*.ipynb) and scripts (*.py).
   • •Find all figures (*.png, *.pdf).
3. •Read Context: Read README.md and PROJECT.md to understand the project goals.

Phase 2: Journal Template Selection

Ask the user for the target journal. Based on the response, adopt the corresponding structure:

Option A: Nature Methods

• •Structure: Introduction -> Results -> Discussion -> Methods.
• •Focus: Novelty, Comparison to SOTA.
• •Constraints: Methods section limited; move extensive details to Supplementary.

Option B: PLOS Computational Biology

• •Structure: Abstract -> Author Summary -> Introduction -> Results -> Discussion -> Methods.
• •Focus: Reproducibility, Biological Insight.
• •Constraints: Mandatory "Author Summary" (non-technical).

Option C: Bioinformatics

• •Structure: Abstract -> Intro -> Algorithm -> Implementation -> Discussion.
• •Focus: Software utility, Performance benchmarks.

Phase 3: Outline Synthesis

Generate a file named manuscript/outline.md. For each section in the template:

1. •Write a Description: What represents the core argument of this section?
2. •Link Files: Explicitly list the relative paths of the code/data files that support this section.
   • •Example: "Results > Section 2.1: Performance. Supports: results/accuracy_table.csv, figures/fig2_roc.png."
3. •Word Count Target: Specify estimated word count for each section.

Required Structure (per schema: schemas/manuscript.yaml)

The outline MUST include:

• •Filename: manuscript/outline.md
• •Target journal specification
• •Sections with:
  • •Section name (Abstract, Introduction, Methods, Results, Discussion)
  • •Word count targets
  • •Evidence files (data, scripts, figures)
  • •Key points to cover

Output and Validation

1. •Create manuscript/outline.md with the structured plan
2. •Validate the outline:
   bash

   python scripts/rrwrite-validate-manuscript.py --file manuscript/outline.md --type outline
   

3. •Update workflow state (mark planning stage as completed):
   python

   import sys
   from pathlib import Path
   sys.path.insert(0, str(Path('scripts').resolve()))
   from rrwrite_state_manager import StateManager
   
   manager = StateManager()
   manager.update_workflow_stage("plan", status="completed", file_path="manuscript/outline.md")
   

4. •Display progress:
   bash

   python scripts/rrwrite-status.py
   

5. •If validation passes, confirm creation and ask user to review
6. •If validation fails, fix issues and re-validate

Confirm the creation of manuscript/outline.md and validation status. Show the updated workflow status.