scientific-writer 2.3.1__py3-none-any.whl

scientific_writer/.claude/skills/peer-review/SKILL.md

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+---
+name: peer-review
+description: "Systematic peer review toolkit. Evaluate methodology, statistics, design, reproducibility, ethics, figure integrity, reporting standards, for manuscript and grant review across disciplines."
+---
+
+# Scientific Critical Evaluation and Peer Review
+
+## Overview
+
+Peer review is a systematic process for evaluating scientific manuscripts. Assess methodology, statistics, design, reproducibility, ethics, and reporting standards. Apply this skill for manuscript and grant review across disciplines with constructive, rigorous evaluation.
+
+## When to Use This Skill
+
+This skill should be used when:
+- Conducting peer review of scientific manuscripts for journals
+- Evaluating grant proposals and research applications
+- Assessing methodology and experimental design rigor
+- Reviewing statistical analyses and reporting standards
+- Evaluating reproducibility and data availability
+- Checking compliance with reporting guidelines (CONSORT, STROBE, PRISMA)
+- Providing constructive feedback on scientific writing
+
+## Peer Review Workflow
+
+Conduct peer review systematically through the following stages, adapting depth and focus based on the manuscript type and discipline.
+
+### Stage 1: Initial Assessment
+
+Begin with a high-level evaluation to determine the manuscript's scope, novelty, and overall quality.
+
+**Key Questions:**
+- What is the central research question or hypothesis?
+- What are the main findings and conclusions?
+- Is the work scientifically sound and significant?
+- Is the work appropriate for the intended venue?
+- Are there any immediate major flaws that would preclude publication?
+
+**Output:** Brief summary (2-3 sentences) capturing the manuscript's essence and initial impression.
+
+### Stage 2: Detailed Section-by-Section Review
+
+Conduct a thorough evaluation of each manuscript section, documenting specific concerns and strengths.
+
+#### Abstract and Title
+- **Accuracy:** Does the abstract accurately reflect the study's content and conclusions?
+- **Clarity:** Is the title specific, accurate, and informative?
+- **Completeness:** Are key findings and methods summarized appropriately?
+- **Accessibility:** Is the abstract comprehensible to a broad scientific audience?
+
+#### Introduction
+- **Context:** Is the background information adequate and current?
+- **Rationale:** Is the research question clearly motivated and justified?
+- **Novelty:** Is the work's originality and significance clearly articulated?
+- **Literature:** Are relevant prior studies appropriately cited?
+- **Objectives:** Are research aims/hypotheses clearly stated?
+
+#### Methods
+- **Reproducibility:** Can another researcher replicate the study from the description provided?
+- **Rigor:** Are the methods appropriate for addressing the research questions?
+- **Detail:** Are protocols, reagents, equipment, and parameters sufficiently described?
+- **Ethics:** Are ethical approvals, consent, and data handling properly documented?
+- **Statistics:** Are statistical methods appropriate, clearly described, and justified?
+- **Validation:** Are controls, replicates, and validation approaches adequate?
+
+**Critical elements to verify:**
+- Sample sizes and power calculations
+- Randomization and blinding procedures
+- Inclusion/exclusion criteria
+- Data collection protocols
+- Computational methods and software versions
+- Statistical tests and correction for multiple comparisons
+
+#### Results
+- **Presentation:** Are results presented logically and clearly?
+- **Figures/Tables:** Are visualizations appropriate, clear, and properly labeled?
+- **Statistics:** Are statistical results properly reported (effect sizes, confidence intervals, p-values)?
+- **Objectivity:** Are results presented without over-interpretation?
+- **Completeness:** Are all relevant results included, including negative results?
+- **Reproducibility:** Are raw data or summary statistics provided?
+
+**Common issues to identify:**
+- Selective reporting of results
+- Inappropriate statistical tests
+- Missing error bars or measures of variability
+- Over-fitting or circular analysis
+- Batch effects or confounding variables
+- Missing controls or validation experiments
+
+#### Discussion
+- **Interpretation:** Are conclusions supported by the data?
+- **Limitations:** Are study limitations acknowledged and discussed?
+- **Context:** Are findings placed appropriately within existing literature?
+- **Speculation:** Is speculation clearly distinguished from data-supported conclusions?
+- **Significance:** Are implications and importance clearly articulated?
+- **Future directions:** Are next steps or unanswered questions discussed?
+
+**Red flags:**
+- Overstated conclusions
+- Ignoring contradictory evidence
+- Causal claims from correlational data
+- Inadequate discussion of limitations
+- Mechanistic claims without mechanistic evidence
+
+#### References
+- **Completeness:** Are key relevant papers cited?
+- **Currency:** Are recent important studies included?
+- **Balance:** Are contrary viewpoints appropriately cited?
+- **Accuracy:** Are citations accurate and appropriate?
+- **Self-citation:** Is there excessive or inappropriate self-citation?
+
+### Stage 3: Methodological and Statistical Rigor
+
+Evaluate the technical quality and rigor of the research with particular attention to common pitfalls.
+
+**Statistical Assessment:**
+- Are statistical assumptions met (normality, independence, homoscedasticity)?
+- Are effect sizes reported alongside p-values?
+- Is multiple testing correction applied appropriately?
+- Are confidence intervals provided?
+- Is sample size justified with power analysis?
+- Are parametric vs. non-parametric tests chosen appropriately?
+- Are missing data handled properly?
+- Are exploratory vs. confirmatory analyses distinguished?
+
+**Experimental Design:**
+- Are controls appropriate and adequate?
+- Is replication sufficient (biological and technical)?
+- Are potential confounders identified and controlled?
+- Is randomization properly implemented?
+- Are blinding procedures adequate?
+- Is the experimental design optimal for the research question?
+
+**Computational/Bioinformatics:**
+- Are computational methods clearly described and justified?
+- Are software versions and parameters documented?
+- Is code made available for reproducibility?
+- Are algorithms and models validated appropriately?
+- Are assumptions of computational methods met?
+- Is batch correction applied appropriately?
+
+### Stage 4: Reproducibility and Transparency
+
+Assess whether the research meets modern standards for reproducibility and open science.
+
+**Data Availability:**
+- Are raw data deposited in appropriate repositories?
+- Are accession numbers provided for public databases?
+- Are data sharing restrictions justified (e.g., patient privacy)?
+- Are data formats standard and accessible?
+
+**Code and Materials:**
+- Is analysis code made available (GitHub, Zenodo, etc.)?
+- Are unique materials available or described sufficiently for recreation?
+- Are protocols detailed in sufficient depth?
+
+**Reporting Standards:**
+- Does the manuscript follow discipline-specific reporting guidelines (CONSORT, PRISMA, ARRIVE, MIAME, MINSEQE, etc.)?
+- See `references/reporting_standards.md` for common guidelines
+- Are all elements of the appropriate checklist addressed?
+
+### Stage 5: Figure and Data Presentation
+
+Evaluate the quality, clarity, and integrity of data visualization.
+
+**Quality Checks:**
+- Are figures high resolution and clearly labeled?
+- Are axes properly labeled with units?
+- Are error bars defined (SD, SEM, CI)?
+- Are statistical significance indicators explained?
+- Are color schemes appropriate and accessible (colorblind-friendly)?
+- Are scale bars included for images?
+- Is data visualization appropriate for the data type?
+
+**Integrity Checks:**
+- Are there signs of image manipulation (duplications, splicing)?
+- Are Western blots and gels appropriately presented?
+- Are representative images truly representative?
+- Are all conditions shown (no selective presentation)?
+
+**Clarity:**
+- Can figures stand alone with their legends?
+- Is the message of each figure immediately clear?
+- Are there redundant figures or panels?
+- Would data be better presented as tables or figures?
+
+### Stage 6: Ethical Considerations
+
+Verify that the research meets ethical standards and guidelines.
+
+**Human Subjects:**
+- Is IRB/ethics approval documented?
+- Is informed consent described?
+- Are vulnerable populations appropriately protected?
+- Is patient privacy adequately protected?
+- Are potential conflicts of interest disclosed?
+
+**Animal Research:**
+- Is IACUC or equivalent approval documented?
+- Are procedures humane and justified?
+- Are the 3Rs (replacement, reduction, refinement) considered?
+- Are euthanasia methods appropriate?
+
+**Research Integrity:**
+- Are there concerns about data fabrication or falsification?
+- Is authorship appropriate and justified?
+- Are competing interests disclosed?
+- Is funding source disclosed?
+- Are there concerns about plagiarism or duplicate publication?
+
+### Stage 7: Writing Quality and Clarity
+
+Assess the manuscript's clarity, organization, and accessibility.
+
+**Structure and Organization:**
+- Is the manuscript logically organized?
+- Do sections flow coherently?
+- Are transitions between ideas clear?
+- Is the narrative compelling and clear?
+
+**Writing Quality:**
+- Is the language clear, precise, and concise?
+- Are jargon and acronyms minimized and defined?
+- Is grammar and spelling correct?
+- Are sentences unnecessarily complex?
+- Is the passive voice overused?
+
+**Accessibility:**
+- Can a non-specialist understand the main findings?
+- Are technical terms explained?
+- Is the significance clear to a broad audience?
+
+## Structuring Peer Review Reports
+
+Organize feedback in a hierarchical structure that prioritizes issues and provides actionable guidance.
+
+### Summary Statement
+
+Provide a concise overall assessment (1-2 paragraphs):
+- Brief synopsis of the research
+- Overall recommendation (accept, minor revisions, major revisions, reject)
+- Key strengths (2-3 bullet points)
+- Key weaknesses (2-3 bullet points)
+- Bottom-line assessment of significance and soundness
+
+### Major Comments
+
+List critical issues that significantly impact the manuscript's validity, interpretability, or significance. Number these sequentially for easy reference.
+
+**Major comments typically include:**
+- Fundamental methodological flaws
+- Inappropriate statistical analyses
+- Unsupported or overstated conclusions
+- Missing critical controls or experiments
+- Serious reproducibility concerns
+- Major gaps in literature coverage
+- Ethical concerns
+
+**For each major comment:**
+1. Clearly state the issue
+2. Explain why it's problematic
+3. Suggest specific solutions or additional experiments
+4. Indicate if addressing it is essential for publication
+
+### Minor Comments
+
+List less critical issues that would improve clarity, completeness, or presentation. Number these sequentially.
+
+**Minor comments typically include:**
+- Unclear figure labels or legends
+- Missing methodological details
+- Typographical or grammatical errors
+- Suggestions for improved data presentation
+- Minor statistical reporting issues
+- Supplementary analyses that would strengthen conclusions
+- Requests for clarification
+
+**For each minor comment:**
+1. Identify the specific location (section, paragraph, figure)
+2. State the issue clearly
+3. Suggest how to address it
+
+### Specific Line-by-Line Comments (Optional)
+
+For manuscripts requiring detailed feedback, provide section-specific or line-by-line comments:
+- Reference specific page/line numbers or sections
+- Note factual errors, unclear statements, or missing citations
+- Suggest specific edits for clarity
+
+### Questions for Authors
+
+List specific questions that need clarification:
+- Methodological details that are unclear
+- Seemingly contradictory results
+- Missing information needed to evaluate the work
+- Requests for additional data or analyses
+
+## Tone and Approach
+
+Maintain a constructive, professional, and collegial tone throughout the review.
+
+**Best Practices:**
+- **Be constructive:** Frame criticism as opportunities for improvement
+- **Be specific:** Provide concrete examples and actionable suggestions
+- **Be balanced:** Acknowledge strengths as well as weaknesses
+- **Be respectful:** Remember that authors have invested significant effort
+- **Be objective:** Focus on the science, not the scientists
+- **Be thorough:** Don't overlook issues, but prioritize appropriately
+- **Be clear:** Avoid ambiguous or vague criticism
+
+**Avoid:**
+- Personal attacks or dismissive language
+- Sarcasm or condescension
+- Vague criticism without specific examples
+- Requesting unnecessary experiments beyond the scope
+- Demanding adherence to personal preferences vs. best practices
+- Revealing your identity if reviewing is double-blind
+
+## Special Considerations by Manuscript Type
+
+### Original Research Articles
+- Emphasize rigor, reproducibility, and novelty
+- Assess significance and impact
+- Verify that conclusions are data-driven
+- Check for complete methods and appropriate controls
+
+### Reviews and Meta-Analyses
+- Evaluate comprehensiveness of literature coverage
+- Assess search strategy and inclusion/exclusion criteria
+- Verify systematic approach and lack of bias
+- Check for critical analysis vs. mere summarization
+- For meta-analyses, evaluate statistical approach and heterogeneity
+
+### Methods Papers
+- Emphasize validation and comparison to existing methods
+- Assess reproducibility and availability of protocols/code
+- Evaluate improvements over existing approaches
+- Check for sufficient detail for implementation
+
+### Short Reports/Letters
+- Adapt expectations for brevity
+- Ensure core findings are still rigorous and significant
+- Verify that format is appropriate for findings
+
+### Preprints
+- Recognize that these have not undergone formal peer review
+- May be less polished than journal submissions
+- Still apply rigorous standards for scientific validity
+- Consider providing constructive feedback to help authors improve before journal submission
+
+## Resources
+
+This skill includes reference materials to support comprehensive peer review:
+
+### references/reporting_standards.md
+Guidelines for major reporting standards across disciplines (CONSORT, PRISMA, ARRIVE, MIAME, STROBE, etc.) to evaluate completeness of methods and results reporting.
+
+### references/common_issues.md
+Catalog of frequent methodological and statistical issues encountered in peer review, with guidance on identifying and addressing them.
+
+## Final Checklist
+
+Before finalizing the review, verify:
+
+- [ ] Summary statement clearly conveys overall assessment
+- [ ] Major concerns are clearly identified and justified
+- [ ] Suggested revisions are specific and actionable
+- [ ] Minor issues are noted but properly categorized
+- [ ] Statistical methods have been evaluated
+- [ ] Reproducibility and data availability assessed
+- [ ] Ethical considerations verified
+- [ ] Figures and tables evaluated for quality and integrity
+- [ ] Writing quality assessed
+- [ ] Tone is constructive and professional throughout
+- [ ] Review is thorough but proportionate to manuscript scope
+- [ ] Recommendation is consistent with identified issues