bio-manuscript-refine

name	bio-manuscript-refine
description	Refinement loop for the bio-manuscript pipeline: three-reviewer iterative optimization (editor, computational, biological). Use when reviewing a manuscript plan, producing structured review comments, revising round by round, and tracking score and revision history toward a target journal.

bio-manuscript-refine

Refine loop: three-reviewer iterative refinement (三审稿人迭代优化)

Run a reviewer-style refinement loop over the manuscript plan using three perspectives: editor, computational reviewer, and biological reviewer.

Purpose

1. Review the current manuscript plan
2. Produce structured review comments
3. Revise the proposal round by round
4. Track score history and revision history

Input Format

manuscript_plan: [full manuscript plan generated in previous steps]
target_journal: [target journal, default nat-communications]
num_rounds: [number of refine rounds, default 2]

Workflow

Round 0

• save the initial proposal snapshot

Each review round

Produce three reviews:

1. Editor
   • novelty
   • feasibility
   • journal fit
2. Computational reviewer
   • method design
   • technical rigor
   • benchmark quality
   • implementation feasibility
3. Biological reviewer
   • biological significance
   • analysis design
   • dataset suitability

Then generate:

• a review summary
• a revision response
• a refined proposal

Output Format

# Refine Report

## Round 0
- initial proposal snapshot

## Round 1 Reviews
### Editor
- scores:
- key concerns:

### Computational Reviewer
- scores:
- key concerns:

### Biological Reviewer
- scores:
- key concerns:

## Round 1 Revision
- addressed concerns:
- remaining risks:

## Score History
| Round | Editor | Computational | Biological | Overall |
|-------|--------|---------------|------------|---------|
| 0 | ... | ... | ... | ... |

## Final Proposal Status
- ready for next phase / needs more revision

Reviewer Criteria

Editor

• novelty
• feasibility
• journal fit

Computational reviewer

• algorithmic soundness
• method novelty
• benchmark rigor
• code feasibility

Biological reviewer

• biological significance
• analysis relevance
• dataset realism

Usage

/bio-manuscript-refine "manuscript_plan: [path to proposal] | target_journal: nat-communications | num_rounds: 2"

Notes

1. Revision should update the proposal itself, not only append comments.
2. Keep a full history of each round.
3. Scores are guidance, not absolute truth; comments matter more than raw numbers.