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Assess methodology, statistics, design, reproducibility, ethics, and reporting standards. Apply this skill for manuscript and grant review across disciplines with constructive, rigorous evaluation.\n\n## When to Use This Skill\n\nThis skill should be used when:\n- Conducting peer review of scientific manuscripts for journals\n- Evaluating grant proposals and research applications\n- Assessing methodology and experimental design rigor\n- Reviewing statistical analyses and reporting standards\n- Evaluating reproducibility and data availability\n- Checking compliance with reporting guidelines (CONSORT, STROBE, PRISMA)\n- Providing constructive feedback on scientific writing\n\n## Visual Enhancement with Scientific Schematics\n\n**When creating documents with this skill, always consider adding scientific diagrams and schematics to enhance visual communication.**\n\nIf your document does not already contain schematics or diagrams:\n- Use the **scientific-schematics** skill to generate AI-powered publication-quality diagrams\n- Simply describe your desired diagram in natural language\n- Nano Banana Pro will automatically generate, review, and refine the schematic\n\n**For new documents:** Scientific schematics should be generated by default to visually represent key concepts, workflows, architectures, or relationships described in the text.\n\n**How to generate schematics:**\n```bash\npython scripts\u002Fgenerate_schematic.py \"your diagram description\" -o figures\u002Foutput.png\n```\n\nThe AI will automatically:\n- Create publication-quality images with proper formatting\n- Review and refine through multiple iterations\n- Ensure accessibility (colorblind-friendly, high contrast)\n- Save outputs in the figures\u002F directory\n\n**When to add schematics:**\n- Peer review workflow diagrams\n- Evaluation criteria decision trees\n- Review process flowcharts\n- Methodology assessment frameworks\n- Quality assessment visualizations\n- Reporting guidelines compliance diagrams\n- Any complex concept that benefits from visualization\n\nFor detailed guidance on creating schematics, refer to the scientific-schematics skill documentation.\n\n---\n\n## Peer Review Workflow\n\nConduct peer review systematically through the following stages, adapting depth and focus based on the manuscript type and discipline.\n\n### Stage 1: Initial Assessment\n\nBegin with a high-level evaluation to determine the manuscript's scope, novelty, and overall quality.\n\n**Key Questions:**\n- What is the central research question or hypothesis?\n- What are the main findings and conclusions?\n- Is the work scientifically sound and significant?\n- Is the work appropriate for the intended venue?\n- Are there any immediate major flaws that would preclude publication?\n\n**Output:** Brief summary (2-3 sentences) capturing the manuscript's essence and initial impression.\n\n### Stage 2: Detailed Section-by-Section Review\n\nConduct a thorough evaluation of each manuscript section, documenting specific concerns and strengths.\n\n#### Abstract and Title\n- **Accuracy:** Does the abstract accurately reflect the study's content and conclusions?\n- **Clarity:** Is the title specific, accurate, and informative?\n- **Completeness:** Are key findings and methods summarized appropriately?\n- **Accessibility:** Is the abstract comprehensible to a broad scientific audience?\n\n#### Introduction\n- **Context:** Is the background information adequate and current?\n- **Rationale:** Is the research question clearly motivated and justified?\n- **Novelty:** Is the work's originality and significance clearly articulated?\n- **Literature:** Are relevant prior studies appropriately cited?\n- **Objectives:** Are research aims\u002Fhypotheses clearly stated?\n\n#### Methods\n- **Reproducibility:** Can another researcher replicate the study from the description provided?\n- **Rigor:** Are the methods appropriate for addressing the research questions?\n- **Detail:** Are protocols, reagents, equipment, and parameters sufficiently described?\n- **Ethics:** Are ethical approvals, consent, and data handling properly documented?\n- **Statistics:** Are statistical methods appropriate, clearly described, and justified?\n- **Validation:** Are controls, replicates, and validation approaches adequate?\n\n**Critical elements to verify:**\n- Sample sizes and power calculations\n- Randomization and blinding procedures\n- Inclusion\u002Fexclusion criteria\n- Data collection protocols\n- Computational methods and software versions\n- Statistical tests and correction for multiple comparisons\n\n#### Results\n- **Presentation:** Are results presented logically and clearly?\n- **Figures\u002FTables:** Are visualizations appropriate, clear, and properly labeled?\n- **Statistics:** Are statistical results properly reported (effect sizes, confidence intervals, p-values)?\n- **Objectivity:** Are results presented without over-interpretation?\n- **Completeness:** Are all relevant results included, including negative results?\n- **Reproducibility:** Are raw data or summary statistics provided?\n\n**Common issues to identify:**\n- Selective reporting of results\n- Inappropriate statistical tests\n- Missing error bars or measures of variability\n- Over-fitting or circular analysis\n- Batch effects or confounding variables\n- Missing controls or validation experiments\n\n#### Discussion\n- **Interpretation:** Are conclusions supported by the data?\n- **Limitations:** Are study limitations acknowledged and discussed?\n- **Context:** Are findings placed appropriately within existing literature?\n- **Speculation:** Is speculation clearly distinguished from data-supported conclusions?\n- **Significance:** Are implications and importance clearly articulated?\n- **Future directions:** Are next steps or unanswered questions discussed?\n\n**Red flags:**\n- Overstated conclusions\n- Ignoring contradictory evidence\n- Causal claims from correlational data\n- Inadequate discussion of limitations\n- Mechanistic claims without mechanistic evidence\n\n#### References\n- **Completeness:** Are key relevant papers cited?\n- **Currency:** Are recent important studies included?\n- **Balance:** Are contrary viewpoints appropriately cited?\n- **Accuracy:** Are citations accurate and appropriate?\n- **Self-citation:** Is there excessive or inappropriate self-citation?\n\n### Stage 3: Methodological and Statistical Rigor\n\nEvaluate the technical quality and rigor of the research with particular attention to common pitfalls.\n\n**Statistical Assessment:**\n- Are statistical assumptions met (normality, independence, homoscedasticity)?\n- Are effect sizes reported alongside p-values?\n- Is multiple testing correction applied appropriately?\n- Are confidence intervals provided?\n- Is sample size justified with power analysis?\n- Are parametric vs. non-parametric tests chosen appropriately?\n- Are missing data handled properly?\n- Are exploratory vs. confirmatory analyses distinguished?\n\n**Experimental Design:**\n- Are controls appropriate and adequate?\n- Is replication sufficient (biological and technical)?\n- Are potential confounders identified and controlled?\n- Is randomization properly implemented?\n- Are blinding procedures adequate?\n- Is the experimental design optimal for the research question?\n\n**Computational\u002FBioinformatics:**\n- Are computational methods clearly described and justified?\n- Are software versions and parameters documented?\n- Is code made available for reproducibility?\n- Are algorithms and models validated appropriately?\n- Are assumptions of computational methods met?\n- Is batch correction applied appropriately?\n\n### Stage 4: Reproducibility and Transparency\n\nAssess whether the research meets modern standards for reproducibility and open science.\n\n**Data Availability:**\n- Are raw data deposited in appropriate repositories?\n- Are accession numbers provided for public databases?\n- Are data sharing restrictions justified (e.g., patient privacy)?\n- Are data formats standard and accessible?\n\n**Code and Materials:**\n- Is analysis code made available (GitHub, Zenodo, etc.)?\n- Are unique materials available or described sufficiently for recreation?\n- Are protocols detailed in sufficient depth?\n\n**Reporting Standards:**\n- Does the manuscript follow discipline-specific reporting guidelines (CONSORT, PRISMA, ARRIVE, MIAME, MINSEQE, etc.)?\n- See `references\u002Freporting_standards.md` for common guidelines\n- Are all elements of the appropriate checklist addressed?\n\n### Stage 5: Figure and Data Presentation\n\nEvaluate the quality, clarity, and integrity of data visualization.\n\n**Quality Checks:**\n- Are figures high resolution and clearly labeled?\n- Are axes properly labeled with units?\n- Are error bars defined (SD, SEM, CI)?\n- Are statistical significance indicators explained?\n- Are color schemes appropriate and accessible (colorblind-friendly)?\n- Are scale bars included for images?\n- Is data visualization appropriate for the data type?\n\n**Integrity Checks:**\n- Are there signs of image manipulation (duplications, splicing)?\n- Are Western blots and gels appropriately presented?\n- Are representative images truly representative?\n- Are all conditions shown (no selective presentation)?\n\n**Clarity:**\n- Can figures stand alone with their legends?\n- Is the message of each figure immediately clear?\n- Are there redundant figures or panels?\n- Would data be better presented as tables or figures?\n\n### Stage 6: Ethical Considerations\n\nVerify that the research meets ethical standards and guidelines.\n\n**Human Subjects:**\n- Is IRB\u002Fethics approval documented?\n- Is informed consent described?\n- Are vulnerable populations appropriately protected?\n- Is patient privacy adequately protected?\n- Are potential conflicts of interest disclosed?\n\n**Animal Research:**\n- Is IACUC or equivalent approval documented?\n- Are procedures humane and justified?\n- Are the 3Rs (replacement, reduction, refinement) considered?\n- Are euthanasia methods appropriate?\n\n**Research Integrity:**\n- Are there concerns about data fabrication or falsification?\n- Is authorship appropriate and justified?\n- Are competing interests disclosed?\n- Is funding source disclosed?\n- Are there concerns about plagiarism or duplicate publication?\n\n### Stage 7: Writing Quality and Clarity\n\nAssess the manuscript's clarity, organization, and accessibility.\n\n**Structure and Organization:**\n- Is the manuscript logically organized?\n- Do sections flow coherently?\n- Are transitions between ideas clear?\n- Is the narrative compelling and clear?\n\n**Writing Quality:**\n- Is the language clear, precise, and concise?\n- Are jargon and acronyms minimized and defined?\n- Is grammar and spelling correct?\n- Are sentences unnecessarily complex?\n- Is the passive voice overused?\n\n**Accessibility:**\n- Can a non-specialist understand the main findings?\n- Are technical terms explained?\n- Is the significance clear to a broad audience?\n\n## Structuring Peer Review Reports\n\nOrganize feedback in a hierarchical structure that prioritizes issues and provides actionable guidance.\n\n### Summary Statement\n\nProvide a concise overall assessment (1-2 paragraphs):\n- Brief synopsis of the research\n- Overall recommendation (accept, minor revisions, major revisions, reject)\n- Key strengths (2-3 bullet points)\n- Key weaknesses (2-3 bullet points)\n- Bottom-line assessment of significance and soundness\n\n### Major Comments\n\nList critical issues that significantly impact the manuscript's validity, interpretability, or significance. Number these sequentially for easy reference.\n\n**Major comments typically include:**\n- Fundamental methodological flaws\n- Inappropriate statistical analyses\n- Unsupported or overstated conclusions\n- Missing critical controls or experiments\n- Serious reproducibility concerns\n- Major gaps in literature coverage\n- Ethical concerns\n\n**For each major comment:**\n1. Clearly state the issue\n2. Explain why it's problematic\n3. Suggest specific solutions or additional experiments\n4. Indicate if addressing it is essential for publication\n\n### Minor Comments\n\nList less critical issues that would improve clarity, completeness, or presentation. Number these sequentially.\n\n**Minor comments typically include:**\n- Unclear figure labels or legends\n- Missing methodological details\n- Typographical or grammatical errors\n- Suggestions for improved data presentation\n- Minor statistical reporting issues\n- Supplementary analyses that would strengthen conclusions\n- Requests for clarification\n\n**For each minor comment:**\n1. Identify the specific location (section, paragraph, figure)\n2. State the issue clearly\n3. Suggest how to address it\n\n### Specific Line-by-Line Comments (Optional)\n\nFor manuscripts requiring detailed feedback, provide section-specific or line-by-line comments:\n- Reference specific page\u002Fline numbers or sections\n- Note factual errors, unclear statements, or missing citations\n- Suggest specific edits for clarity\n\n### Questions for Authors\n\nList specific questions that need clarification:\n- Methodological details that are unclear\n- Seemingly contradictory results\n- Missing information needed to evaluate the work\n- Requests for additional data or analyses\n\n## Tone and Approach\n\nMaintain a constructive, professional, and collegial tone throughout the review.\n\n**Best Practices:**\n- **Be constructive:** Frame criticism as opportunities for improvement\n- **Be specific:** Provide concrete examples and actionable suggestions\n- **Be balanced:** Acknowledge strengths as well as weaknesses\n- **Be respectful:** Remember that authors have invested significant effort\n- **Be objective:** Focus on the science, not the scientists\n- **Be thorough:** Don't overlook issues, but prioritize appropriately\n- **Be clear:** Avoid ambiguous or vague criticism\n\n**Avoid:**\n- Personal attacks or dismissive language\n- Sarcasm or condescension\n- Vague criticism without specific examples\n- Requesting unnecessary experiments beyond the scope\n- Demanding adherence to personal preferences vs. best practices\n- Revealing your identity if reviewing is double-blind\n\n## Special Considerations by Manuscript Type\n\n### Original Research Articles\n- Emphasize rigor, reproducibility, and novelty\n- Assess significance and impact\n- Verify that conclusions are data-driven\n- Check for complete methods and appropriate controls\n\n### Reviews and Meta-Analyses\n- Evaluate comprehensiveness of literature coverage\n- Assess search strategy and inclusion\u002Fexclusion criteria\n- Verify systematic approach and lack of bias\n- Check for critical analysis vs. mere summarization\n- For meta-analyses, evaluate statistical approach and heterogeneity\n\n### Methods Papers\n- Emphasize validation and comparison to existing methods\n- Assess reproducibility and availability of protocols\u002Fcode\n- Evaluate improvements over existing approaches\n- Check for sufficient detail for implementation\n\n### Short Reports\u002FLetters\n- Adapt expectations for brevity\n- Ensure core findings are still rigorous and significant\n- Verify that format is appropriate for findings\n\n### Preprints\n- Recognize that these have not undergone formal peer review\n- May be less polished than journal submissions\n- Still apply rigorous standards for scientific validity\n- Consider providing constructive feedback to help authors improve before journal submission\n\n### Presentations and Slide Decks\n\n**⚠️ CRITICAL: For presentations, NEVER read the PDF directly. ALWAYS convert to images first.**\n\nWhen reviewing scientific presentations (PowerPoint, Beamer, slide decks):\n\n#### Mandatory Image-Based Review Workflow\n\n**NEVER attempt to read presentation PDFs directly** - this causes buffer overflow errors and doesn't show visual formatting issues.\n\n**Required Process:**\n1. Convert PDF to images using Python:\n   ```bash\n   python skills\u002Fscientific-slides\u002Fscripts\u002Fpdf_to_images.py presentation.pdf review\u002Fslide --dpi 150\n   # Creates: review\u002Fslide-001.jpg, review\u002Fslide-002.jpg, etc.\n   ```\n2. Read and inspect EACH slide image file sequentially\n3. Document issues with specific slide numbers\n4. Provide feedback on visual formatting and content\n\n**Print when starting review:**\n```\n[HH:MM:SS] PEER REVIEW: Presentation detected - converting to images for review\n[HH:MM:SS] PDF REVIEW: NEVER reading PDF directly - using image-based inspection\n```\n\n#### Presentation-Specific Evaluation Criteria\n\n**Visual Design and Readability:**\n- [ ] Text is large enough (minimum 18pt, ideally 24pt+ for body text)\n- [ ] High contrast between text and background (4.5:1 minimum, 7:1 preferred)\n- [ ] Color scheme is professional and colorblind-accessible\n- [ ] Consistent visual design across all slides\n- [ ] White space is adequate (not cramped)\n- [ ] Fonts are clear and professional\n\n**Layout and Formatting (Check EVERY Slide Image):**\n- [ ] No text overflow or truncation at slide edges\n- [ ] No element overlaps (text over images, overlapping shapes)\n- [ ] Titles are consistently positioned\n- [ ] Content is properly aligned\n- [ ] Bullets and text are not cut off\n- [ ] Figures fit within slide boundaries\n- [ ] Captions and labels are visible and readable\n\n**Content Quality:**\n- [ ] One main idea per slide (not overloaded)\n- [ ] Minimal text (3-6 bullets per slide maximum)\n- [ ] Bullet points are concise (5-7 words each)\n- [ ] Figures are simplified and clear (not copy-pasted from papers)\n- [ ] Data visualizations have large, readable labels\n- [ ] Citations are present and properly formatted\n- [ ] Results\u002Fdata slides dominate the presentation (40-50% of content)\n\n**Structure and Flow:**\n- [ ] Clear narrative arc (introduction → methods → results → discussion)\n- [ ] Logical progression between slides\n- [ ] Slide count appropriate for talk duration (~1 slide per minute)\n- [ ] Title slide includes authors, affiliation, date\n- [ ] Introduction cites relevant background literature (3-5 papers)\n- [ ] Discussion cites comparison papers (3-5 papers)\n- [ ] Conclusions slide summarizes key findings\n- [ ] Acknowledgments\u002Ffunding slide at end\n\n**Scientific Content:**\n- [ ] Research question clearly stated\n- [ ] Methods adequately summarized (not excessive detail)\n- [ ] Results presented logically with clear visualizations\n- [ ] Statistical significance indicated appropriately\n- [ ] Conclusions supported by data shown\n- [ ] Limitations acknowledged where appropriate\n- [ ] Future directions or broader impact discussed\n\n**Common Presentation Issues to Flag:**\n\n**Critical Issues (Must Fix):**\n- Text overflow making content unreadable\n- Font sizes too small (\u003C18pt)\n- Element overlaps obscuring data\n- Insufficient contrast (text hard to read)\n- Figures too complex or illegible\n- No citations (completely unsupported claims)\n- Slide count drastically mismatched to duration\n\n**Major Issues (Should Fix):**\n- Inconsistent design across slides\n- Too much text (walls of text, not bullets)\n- Poorly simplified figures (axis labels too small)\n- Cramped layout with insufficient white space\n- Missing key structural elements (no conclusion slide)\n- Poor color choices (not colorblind-safe)\n- Minimal results content (\u003C30% of slides)\n\n**Minor Issues (Suggestions for Improvement):**\n- Could use more visuals\u002Fdiagrams\n- Some slides slightly text-heavy\n- Minor alignment inconsistencies\n- Could benefit from more white space\n- Additional citations would strengthen claims\n- Color scheme could be more modern\n\n#### Review Report Format for Presentations\n\n**Summary Statement:**\n- Overall impression of presentation quality\n- Appropriateness for target audience and duration\n- Key strengths (visual design, content, clarity)\n- Key weaknesses (formatting issues, content gaps)\n- Recommendation (ready to present, minor revisions, major revisions)\n\n**Layout and Formatting Issues (By Slide Number):**\n```\nSlide 3: Text overflow - bullet point 4 extends beyond right margin\nSlide 7: Element overlap - figure overlaps with caption text\nSlide 12: Font size - axis labels too small to read from distance\nSlide 18: Alignment - title not centered\n```\n\n**Content and Structure Feedback:**\n- Adequacy of background context and citations\n- Clarity of research question and objectives\n- Quality of methods summary\n- Effectiveness of results presentation\n- Strength of conclusions and implications\n\n**Design and Accessibility:**\n- Overall visual appeal and professionalism\n- Color contrast and readability\n- Colorblind accessibility\n- Consistency across slides\n\n**Timing and Scope:**\n- Whether slide count matches intended duration\n- Appropriate level of detail for talk type\n- Balance between sections\n\n#### Example Image-Based Review Process\n\n```\n[14:30:00] PEER REVIEW: Starting review of presentation\n[14:30:05] PEER REVIEW: Presentation detected - converting to images\n[14:30:10] PDF REVIEW: Running pdf_to_images.py on presentation.pdf\n[14:30:15] PDF REVIEW: Converted 25 slides to images in review\u002F directory\n[14:30:20] PDF REVIEW: Inspecting slide 1\u002F25 - title slide\n[14:30:25] PDF REVIEW: Inspecting slide 2\u002F25 - introduction\n...\n[14:35:40] PDF REVIEW: Inspecting slide 25\u002F25 - acknowledgments\n[14:35:45] PDF REVIEW: Completed image-based review\n[14:35:50] PEER REVIEW: Found 8 layout issues, 3 content issues\n[14:35:55] PEER REVIEW: Generating structured feedback by slide number\n```\n\n**Remember:** For presentations, the visual inspection via images is MANDATORY. Never attempt to read presentation PDFs as text - it will fail and miss all visual formatting issues.\n\n## Resources\n\nThis skill includes reference materials to support comprehensive peer review:\n\n### references\u002Freporting_standards.md\nGuidelines for major reporting standards across disciplines (CONSORT, PRISMA, ARRIVE, MIAME, STROBE, etc.) to evaluate completeness of methods and results reporting.\n\n### references\u002Fcommon_issues.md\nCatalog of frequent methodological and statistical issues encountered in peer review, with guidance on identifying and addressing them.\n\n## Final Checklist\n\nBefore finalizing the review, verify:\n\n- [ ] Summary statement clearly conveys overall assessment\n- [ ] Major concerns are clearly identified and justified\n- [ ] Suggested revisions are specific and actionable\n- [ ] Minor issues are noted but properly categorized\n- [ ] Statistical methods have been evaluated\n- [ ] Reproducibility and data availability assessed\n- [ ] Ethical 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