Manuscript Review Panel

Before You Start

1. Read references/personas.md to understand the 13 reviewer personas, their focus areas, and review structures.

2. If you have an Anthropic API key and want to use the automated pipeline, see references/script-usage.md. Otherwise, use Manual Orchestration below (the preferred approach in Cowork and Claude.ai).

Optional: Ask the user what they need

Before launching the full panel, you can ask:

• Target journal or venue? (affects framing advice from editor persona)
• Submission timeline? (affects whether "do more experiments" is useful)
• Specific concerns? (any areas they already know are weak?)
• Which reviewers to emphasize? (they can pick a subset — see Customization)

This is optional — if the user just says "review my paper," run the full panel with sensible defaults.

Manual Orchestration

Run the review by role-playing each agent persona yourself. This is the preferred approach in Cowork and Claude.ai — no API key or script needed.

Manual Phase 1: Read the manuscript carefully

Read the full manuscript. Extract and note:

• The main claim / contribution
• Methods used
• Key results and figures
• Target audience and field

Manual Phase 2: Run each reviewer perspective

For each persona in references/personas.md, adopt that persona's viewpoint and write a review. The minimum useful set is:

Core 7 (always run these):

1. 😈 Devil's Advocate — anticipate hostile reviewer attacks
2. 🔬 Methods & Logic — check technical rigor
3. 📊 Trend Expert — check literature and novelty (USE WEB SEARCH)
4. 🤝 Collaborator — identify what's undersold or missing
5. ✍️ Professional Editor — improve writing and structure
6. 📝 Tech Writer — improve figures and presentation
7. 🏛️ Narrative Architect — build immersive, compelling, logically valid narrative

Extended (run if time allows): 8. 📰 Editor Perspective — journal fit and impact framing 9. 🎯 Strategic Advisor — broader impact narrative 10. 🔭 Adjacent Field — accessibility check 11. 🧪 Lab Colleague — practical quick wins 12. 🚀 Visionary — ambitious framing suggestions 13. 🛠️ Technical Expert — methods optimization

For agents marked with web search, actively search PubMed and the web:

• Search for recent papers on the same topic
• Check if key claims are supported by current literature
• Look for missing references
• Check for competing/overlapping preprints on bioRxiv

Manual Phase 3: Identify and discuss disagreements

After all reviews, compare them and identify where they disagree. For each disagreement:

1. State both positions
2. Classify: factual, methodological preference, or judgment call
3. Give a clear recommendation to the authors

Manual Phase 4: Synthesize the final report

Produce the final report following this structure:

## Executive Summary
(Overview: what works, what needs improvement, top 3 priorities)

## Strengths (Don't Change These)
(What's working well — authors need to know what to preserve)

## Critical Improvements (Must-Do)
(Ranked by impact. Each: issue → why it matters → how to fix)

## Recommended Improvements (Should-Do)
(Important but not deal-breaking)

## Experiments & Analyses to Consider
(Additional work that would strengthen claims. Note feasibility.)

## Writing & Presentation
(Clarity, figures, structure, narrative improvements)

## Literature & Positioning
(Missing refs, novelty concerns, positioning advice)

## Points of Disagreement
(Where panel members disagreed, with discussion)

## Minor Points
(Small fixes)

## Recommended Action Plan
(Prioritized checklist: immediate → short-term → longer-term)

Customization

Running a subset of agents

Users may not need all 13 perspectives. Common subsets:

• Quick review (3 agents): devils_advocate, professional_editor, trend_expert
• Technical deep-dive (4): devils_advocate, methods_obsessive, technical_expert, collaborator
• Writing focus (4): professional_editor, tech_writer, narrative_architect, adjacent_field
• Pre-submission check (7): the Core 7 listed above
• Full panel (13): all agents

Adding context

If the user provides additional context (cover letter, target journal, specific concerns), prepend it to each agent's review prompt so every persona has the same background information.

Using PubMed and bioRxiv searches

Agents with search capability (trend_expert, devils_advocate, technical_expert, methods_obsessive, strategic_advisor, narrative_architect) should actively search PubMed and the web:

• [main topic] [key method] site:pubmed.ncbi.nlm.nih.gov — recent papers
• [topic] site:biorxiv.org — preprints that might scoop or overlap
• [specific claim or method] — fact-checking specific assertions
• [author names] [topic] — the authors' prior related work

When PubMed MCP tools are available, use search_articles with relevant queries.

Output Format

The primary deliverable is an interactive HTML report saved to the user's output directory as review_report_<manuscript_name>.html. A supplementary Markdown version is saved alongside it.

The HTML report supports Mermaid diagrams (action-plan flowcharts, priority matrices, etc.), collapsible reviewer cards, dark mode, and print-friendly layout. For details on producing and customising the HTML output, see references/html-output.md.

The report contains:

1. The synthesized improvement roadmap (the main deliverable)
2. Full individual reviews from each agent (collapsible appendix)
3. Panel discussion notes (appendix)

Present the .html report using present_files, then walk the user through the executive summary and top priorities conversationally.

Important Reminders

• This is for improvement, not judgment. Never frame the output as accept/reject. Frame everything as "here's how to make it stronger."
• Every criticism needs a suggestion. No reviewer should raise a problem without suggesting a solution or workaround.
• Be specific. "The writing needs improvement" is useless. "The third paragraph of the introduction buries the key motivation — lead with the clinical need instead" is actionable.
• Respect the authors' expertise. They know their research better than any AI. Frame suggestions as options, not mandates. Use language like "consider," "the panel suggests," "one approach would be."
• Use web search actively. The trend expert and devil's advocate personas should always search for recent literature. Outdated novelty assessments are worse than none.
• Preserve what works. Explicitly call out strengths. Authors need to know what NOT to change during revision.

Error Handling

• If PDF extraction produces garbled text, try pdfplumber, pymupdf, or rasterize-and-OCR.
• If you can't complete a persona (context too long, etc.), skip it and note the gap. The synthesis can work with incomplete reviews.
• If the manuscript is very long (>50 pages), consider reviewing sections separately or truncating supplementary material.