Agent-Skills.md

Agent Skills: Scientific Peer Review

Systematic peer review and self-evaluation toolkit. Evaluate methodology, statistics, experimental design, reproducibility, ethics, and reporting standards. Use during the REVIEW phase to assess manuscript quality before submission, or when reviewing others' work.

UncategorizedID: braselog/researchassistant/peer-review

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braselog/researchassistant
braselog
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.ra/skills/peer-review/SKILL.md

Skill Metadata

Name
peer-review
Description
Systematic peer review and self-evaluation toolkit. Evaluate methodology, statistics, experimental design, reproducibility, ethics, and reporting standards. Use during the REVIEW phase to assess manuscript quality before submission, or when reviewing others' work.

Scientific Peer Review

Rigorously evaluate scientific work for quality, validity, and reproducibility.

When to Use

  • Self-reviewing manuscript before submission (REVIEW phase)
  • Evaluating methodology and experimental design
  • Checking statistical analyses and reporting
  • Assessing reproducibility and data availability
  • Reviewing others' manuscripts for journals
  • Evaluating grant proposals
  • Quality checking your own work during ANALYSIS phase

Review Workflow

1. INITIAL SCAN      → Overall impression, scope, significance
2. SECTION REVIEW    → Detailed evaluation of each section
3. METHODOLOGY       → Rigor, assumptions, controls
4. STATISTICS        → Appropriate tests, effect sizes, reporting
5. REPRODUCIBILITY   → Data, code, materials availability
6. FIGURES/TABLES    → Clarity, integrity, accessibility
7. ETHICS            → Approvals, consent, conflicts
8. WRITING           → Clarity, organization, accuracy
9. SYNTHESIZE        → Major/minor issues, recommendation

Stage 1: Initial Assessment

Quick Questions (5 minutes)

  1. What is the central research question?
  2. What are the main findings?
  3. Is the work scientifically sound?
  4. Are there any immediate major flaws?
  5. Is it appropriate for the intended venue?

Initial Summary Template

## Initial Assessment

**Research Question**: [One sentence summary]

**Main Findings**: [2-3 key results]

**Initial Impression**: [Sound/Concerning/Major issues]

**Significance**: [Novel contribution to field?]

Stage 2: Section-by-Section Review

Abstract & Title

| Check | Question | Status | |-------|----------|--------| | Accuracy | Does abstract reflect the actual study? | ☐ | | Clarity | Is the title specific and informative? | ☐ | | Completeness | Are key findings summarized? | ☐ | | Accessibility | Understandable to broad audience? | ☐ |

Introduction

| Check | Question | Status | |-------|----------|--------| | Context | Is background adequate and current? | ☐ | | Rationale | Is the research question justified? | ☐ | | Novelty | Is originality clearly stated? | ☐ | | Literature | Are relevant papers cited? | ☐ | | Objectives | Are aims/hypotheses clear? | ☐ |

Methods

| Check | Question | Status | |-------|----------|--------| | Reproducibility | Can another researcher replicate this? | ☐ | | Rigor | Are methods appropriate for the question? | ☐ | | Detail | Protocols, reagents, parameters described? | ☐ | | Ethics | Approvals and consent documented? | ☐ | | Statistics | Methods described and justified? | ☐ | | Controls | Appropriate controls included? | ☐ |

Critical Details to Verify:

  • Sample sizes and power calculations
  • Randomization and blinding
  • Inclusion/exclusion criteria
  • Software versions
  • Statistical tests and corrections

Results

| Check | Question | Status | |-------|----------|--------| | Presentation | Logical and clear? | ☐ | | Figures | Appropriate, clear, labeled? | ☐ | | Statistics | Effect sizes, CIs, p-values? | ☐ | | Objectivity | Results without interpretation? | ☐ | | Completeness | Negative results included? | ☐ |

Common Issues:

  • Selective reporting
  • Inappropriate statistical tests
  • Missing error bars
  • Over-fitting
  • Batch effects or confounders
  • Missing controls

Discussion

| Check | Question | Status | |-------|----------|--------| | Interpretation | Conclusions supported by data? | ☐ | | Limitations | Acknowledged and discussed? | ☐ | | Context | Placed appropriately in literature? | ☐ | | Speculation | Distinguished from data-supported claims? | ☐ | | Significance | Implications clearly stated? | ☐ |

Red Flags:

  • Overstated conclusions
  • Ignoring contradictory evidence
  • Causal claims from correlational data
  • Mechanistic claims without evidence

Stage 3: Methodological Rigor

Statistical Assessment

| Check | Question | Status | |-------|----------|--------| | Assumptions | Are statistical assumptions met? | ☐ | | Effect sizes | Reported alongside p-values? | ☐ | | Multiple testing | Correction applied? | ☐ | | Confidence intervals | Provided? | ☐ | | Sample size | Justified with power analysis? | ☐ | | Missing data | Handled appropriately? | ☐ | | Exploratory vs confirmatory | Clearly distinguished? | ☐ |

Experimental Design

| Check | Question | Status | |-------|----------|--------| | Controls | Appropriate and adequate? | ☐ | | Replication | Biological and technical? | ☐ | | Confounders | Identified and controlled? | ☐ | | Randomization | Properly implemented? | ☐ | | Blinding | Adequate for the study? | ☐ |

Stage 4: Reproducibility Assessment

Data Availability

| Check | Question | Status | |-------|----------|--------| | Raw data | Deposited in repository? | ☐ | | Accession numbers | Provided for databases? | ☐ | | Restrictions | Justified (e.g., privacy)? | ☐ | | Formats | Standard and accessible? | ☐ |

Code and Materials

| Check | Question | Status | |-------|----------|--------| | Analysis code | Available (GitHub, Zenodo)? | ☐ | | Protocols | Detailed enough to reproduce? | ☐ | | Materials | Available or recreatable? | ☐ |

Reporting Standards

Check adherence to discipline-specific guidelines:

| Study Type | Guideline | Status | |------------|-----------|--------| | Randomized trial | CONSORT | ☐ | | Observational | STROBE | ☐ | | Systematic review | PRISMA | ☐ | | Diagnostic study | STARD | ☐ | | Animal research | ARRIVE | ☐ | | Case report | CARE | ☐ |

Stage 5: Figure and Table Review

Quality Checks

| Check | Question | Status | |-------|----------|--------| | Resolution | High quality? | ☐ | | Labels | All axes/columns labeled with units? | ☐ | | Error bars | Defined (SD, SEM, CI)? | ☐ | | Statistics | Significance markers explained? | ☐ | | Color | Colorblind-friendly? | ☐ | | Scale bars | Included for images? | ☐ |

Integrity Checks

| Check | Question | Status | |-------|----------|--------| | Manipulation | Any signs of image manipulation? | ☐ | | Splicing | Gels/blots appropriately presented? | ☐ | | Representative | Images truly representative? | ☐ | | Complete | All conditions shown? | ☐ |

Stage 6: Writing Quality

Structure and Organization

| Check | Question | Status | |-------|----------|--------| | Logic | Manuscript logically organized? | ☐ | | Flow | Sections flow coherently? | ☐ | | Transitions | Clear between ideas? | ☐ | | Narrative | Compelling and clear? | ☐ |

Writing Quality

| Check | Question | Status | |-------|----------|--------| | Clarity | Language clear and precise? | ☐ | | Jargon | Minimized and defined? | ☐ | | Grammar | Correct throughout? | ☐ | | Concise | No unnecessary complexity? | ☐ |

Structuring the Review Report

Summary Statement (1-2 paragraphs)

## Summary

[Brief synopsis of the research]

**Recommendation**: [Accept / Minor revisions / Major revisions / Reject]

**Key Strengths**:
1. [Strength 1]
2. [Strength 2]
3. [Strength 3]

**Key Weaknesses**:
1. [Weakness 1]
2. [Weakness 2]

**Bottom Line**: [Overall assessment of significance and soundness]

Major Comments

Issues that significantly impact validity or interpretability:

## Major Comments

1. **[Issue Title]**
   - *Problem*: [Clear statement of the issue]
   - *Why it matters*: [Impact on conclusions]
   - *Suggestion*: [How to address it]

2. **[Issue Title]**
   ...

Major issues typically include:

  • Fundamental methodological flaws
  • Inappropriate statistical analyses
  • Unsupported conclusions
  • Missing critical controls
  • Reproducibility concerns

Minor Comments

Less critical issues that would improve the manuscript:

## Minor Comments

1. [Page/Figure X]: [Issue and suggestion]
2. [Methods section]: [Missing detail]
3. [Figure 2]: [Clarity improvement]

Review Tone Guidelines

Do ✓

  • Be constructive and specific
  • Acknowledge strengths
  • Provide actionable suggestions
  • Focus on the science
  • Be thorough but proportionate

Don't ✗

  • Use dismissive language
  • Make personal attacks
  • Be vague or sarcastic
  • Request unnecessary experiments
  • Impose personal preferences as requirements

Self-Review Checklist (Before Submission)

Use this during your REVIEW phase:

Methodology

  • [ ] Methods are reproducible
  • [ ] Controls are appropriate and documented
  • [ ] Statistical methods are justified
  • [ ] Sample sizes are adequate

Results

  • [ ] All results support conclusions
  • [ ] Effect sizes are reported
  • [ ] Negative results are included
  • [ ] Figures are clear and accessible

Reproducibility

  • [ ] Data will be available
  • [ ] Code is documented and available
  • [ ] Protocols are detailed
  • [ ] Reporting guidelines followed

Writing

  • [ ] Abstract accurately summarizes the work
  • [ ] Conclusions are supported by data
  • [ ] Limitations are acknowledged
  • [ ] References are current and complete

Integration with RA Workflow

REVIEW Phase Activities

  1. Run self-review using this checklist
  2. Document issues in tasks.md
  3. Address each issue systematically
  4. Re-review until checklist passes
  5. Update .research/logs/activity.md

Pre-Submission Verification

Before calling a manuscript complete:

  • [ ] Self-review completed
  • [ ] All major issues addressed
  • [ ] Figures meet journal requirements
  • [ ] Data/code deposited
  • [ ] Reporting checklist complete
  • [ ] Cover letter prepared