# Jkitchin Skillz Scientific Writing > Scientific Writing - Skill: `tomevault-io/jkitchin-skillz-scientific-writing` (Agent Skill, multi-file: 2 files) - Install (CLI): `npx skillmds@latest add tomevault-io/jkitchin-skillz-scientific-writing` - Raw SKILL.md: https://api.skillmd.com/api/skills/tomevault-io/jkitchin-skillz-scientific-writing/raw - Safety review: pending (external: skill-scanner PASS, skillspector PASS) - Works with: Claude Code, Claude.ai, OpenAI Codex - Category: Coding & Dev Tools - Author: tomevault-io (https://skillmd.com/u/tomevault-io) - Updated: 2026-09-17 - Page: https://skillmd.com/skills/tomevault-io/jkitchin-skillz-scientific-writing --- # Scientific Writing Systematic guidance for writing research papers, grants, and scientific communications with emphasis on clarity, reproducibility, and adherence to field conventions. ## Scientific Writing Workflow ### 1. Identify Document Type and Requirements Determine what you're writing: - Research article → Full paper with novel findings - Review article → Synthesis of existing literature - Grant proposal → Funding application - Conference abstract → Brief standalone summary - Revision response → Reply to peer reviewers - Technical report → Documentation of work Gather venue requirements: - Target journal/conference/funder name - Word/page limits by section - Citation style required - Figure/table format specifications - Submission guidelines and templates ### 2. Select Structure and Route to Guidance For research articles: - Use IMRAD structure (see references/paper-structure.md) - Introduction: references/introduction-writing.md - Methods: references/methods-writing.md - Results: references/results-writing.md - Discussion: references/discussion-writing.md - Abstract: references/abstract-writing.md For review articles: - See references/review-writing.md for thematic organization - Focus on synthesis, not chronological listing - Critical evaluation of literature For grant proposals: - See references/grant-writing.md for funder-specific guidance - Specific Aims structure - Significance, Innovation, Approach For revision responses: - See references/revision-response.md for point-by-point format - Diplomatic language and tracking changes ### 3. Write Section by Section Follow section-specific guidance: Introduction (references/introduction-writing.md) - Funnel structure: Broad → Narrow → Gap → Objective - Establish context and importance - Identify knowledge gap - State clear objective Methods (references/methods-writing.md) - Reproducibility is paramount - Include all essential details: equipment, reagents, software, statistics - Organize chronologically or by subsystem - Past tense, field-appropriate voice Results (references/results-writing.md) - Report observations objectively - No interpretation (save for discussion) - Integrate figures and tables - Include statistical details - Past tense Discussion (references/discussion-writing.md) - Interpret findings in context - Compare with literature - Acknowledge limitations honestly - Discuss implications and future work - Mix of present (facts) and past (your results) ### 4. Create Figures and Tables Figures (references/figure-design.md) - Match figure type to data type - Publication quality: 300+ DPI, readable fonts, vector when possible - Complete captions with all essential information - Colorblind-friendly palettes Tables (references/table-design.md) - Use when precise values needed - Clear headers with units - Consistent decimal places - Descriptive captions Tools: ```bash # Generate publication-quality figures python scripts/figure_generator.py data.csv config.yaml --output fig1.pdf # Format tables for journals python scripts/table_formatter.py data.csv --format latex --journal nature ``` ### 5. Manage Citations and References Citation formatting (references/citation-management.md) - Match journal's required style: - Numbered: [1], [2,3], [1-5] - Author-year: (Smith, 2020; Jones, 2021) - Author-number: Smith (1) - Check all in-text citations have references - Check all references are cited - Consistent formatting throughout Tools: ```bash # Validate citation consistency python scripts/citation_checker.py manuscript.docx --style apa ``` ### 6. Improve Clarity and Conciseness Language clarity (references/language-clarity.md) - Active voice preferred (field norms vary) - Concise: remove filler words and redundancies - Precise: avoid vague terms ("very," "quite," "many") - One main idea per sentence - Logical paragraph flow Tools: ```bash # Analyze readability python scripts/readability_analyzer.py section.txt # Count words by section python scripts/word_counter.py manuscript.docx ``` ### 7. Review Against Requirements Pre-submission checklist: - [ ] Word limits met for each section - [ ] All figures/tables referenced in text - [ ] All citations formatted consistently - [ ] Statistical details complete - [ ] Methods reproducible - [ ] Limitations discussed - [ ] Abstract within word limit - [ ] Keywords selected - [ ] Author contributions stated - [ ] Conflicts of interest disclosed - [ ] Data availability statement - [ ] Ethics approvals included ## Document Type Routing ### Research Article → IMRAD Structure Structure overview (references/paper-structure.md) IMRAD sections: - /I/ntroduction: Background, gap, objective - /M/ethods: Reproducible experimental details - /R/esults: Objective observations with data - /A/nd - /D/iscussion: Interpretation, implications, limitations What goes where: - Introduction: Why this work matters, what's unknown, what you'll do - Methods: How you did it (enough detail to reproduce) - Results: What you found (observations, not interpretations) - Discussion: What it means, how it fits, what's next Common mistakes to avoid: - ❌ Interpretation in results section - ❌ New results in discussion section - ❌ Methods scattered in results - ❌ Missing gap identification in introduction - ❌ Ignoring limitations ### Review Article → Thematic Organization See references/review-writing.md Types: - Narrative review: Broad overview - Systematic review: Structured search (PRISMA) - Meta-analysis: Quantitative synthesis Key principles: - Synthesize thematically, not chronologically - Critical evaluation, not just summary - Identify patterns, gaps, controversies - Future directions ### Grant Proposal → Funder-Specific Structure See references/grant-writing.md Common elements: - Specific Aims (1 page): Clear, testable objectives - Significance: Why it matters, current knowledge, impact - Innovation: What's novel about approach - Approach: Methods, timeline, pitfalls, alternatives - Preliminary data: Feasibility demonstration Review criteria alignment: - Address all criteria explicitly - Use headings matching criteria - Make reviewers' job easy ### Revision Response → Point-by-Point See references/revision-response.md Structure: - Thank reviewers - Summary of major changes - Point-by-point responses with line numbers - Track changes in manuscript Response strategies: - Agree and comply: Describe changes made - Agree but can't comply: Explain why, offer alternative - Disagree: Provide evidence diplomatically ## Section-Specific Guidance ### Introduction Writing See references/introduction-writing.md Funnel structure: 1. Broad context (why general topic matters) 2. Narrow to specific problem area 3. Identify gap in knowledge 4. State objective of this work 5. Brief approach overview (optional) Length: Typically 1-3 pages Tense: Present for established facts, past for previous studies ### Methods Writing See references/methods-writing.md Reproducibility checklist: - Equipment: manufacturer, model, specs - Reagents: source, catalog #, concentration - Software: name, version, parameters - Statistical tests with corrections - Sample size justification - Ethics approvals Organization: - Chronological (when order matters) - By subsystem (complex systems) - By measurement type (multiple assays) Detail level: - Standard procedures: Brief + citation - Novel procedures: Full detail - Modified procedures: Highlight changes ### Results Writing See references/results-writing.md Objectivity principles: - Report observations, not interpretations - "Data show" not "data prove" - Present negative results honestly - Save interpretation for discussion Statistical reporting: - Test statistic, df, exact p-value - Effect sizes and confidence intervals - Multiple comparison corrections - Measures of variability (SD, SE, CI) Figure integration: - Reference every figure/table in text - Describe key finding from each - Don't just say "see Figure X" ### Discussion Writing See references/discussion-writing.md Structure: 1. Restate main findings (brief) 2. Interpret in context of literature 3. Compare with previous work 4. Explain unexpected findings 5. Acknowledge limitations 6. Discuss implications 7. Suggest future directions Limitations: - Be honest but not self-defeating - Explain impact of limitations - Suggest how to address - Don't introduce obscure limitations ### Abstract Writing See references/abstract-writing.md Essential elements: - Background (1-2 sentences) - Objective - Methods (brief approach) - Results (key findings with data) - Conclusions (significance) Word limit strategies: - Typical: 150-300 words - Prioritize results and conclusions - Remove modifiers - Define abbreviations sparingly - No citations (usually) Self-contained requirement: - Understandable without reading paper - Include actual data, not just "significant" ## Universal Scientific Writing Principles ### 1. Clarity Over Complexity - Simple words over complex when meaning is same - Short sentences preferred - One idea per sentence - Active voice when possible (field norms vary) - Define specialized terms ### 2. Precision in Language - Specific numbers over vague terms - "Approximately 50%" not "many" - Distinguish "significant" (statistical) from "important" - Clear about causation vs correlation - Avoid hedging excessively ("relatively," "quite," "very") ### 3. Objectivity in Reporting - Separate observations (results) from interpretations (discussion) - Present negative results honestly - Acknowledge contradictory evidence - Don't overstate conclusions - Appropriate level of certainty ### 4. Reproducibility in Methods - Include all information needed to reproduce - Equipment specifications - Exact concentrations and conditions - Statistical methods fully described - Software versions and parameters - Code availability when applicable ### 5. Logical Flow of Argument - Each section builds on previous - Clear transitions between ideas - Coherent narrative throughout - Introduction sets up discussion - Discussion answers introduction's questions ### 6. Appropriate Detail for Audience - Assume audience has field background - Define specialized terms first use - Balance between too much and too little detail - Don't explain fundamental concepts - Do explain novel techniques or applications ## Tense and Voice Usage Guide ### Tense by Section Introduction: - Present: Established facts ("DNA is composed of...") - Past: Previous studies ("Smith et al. showed...") - Present: Your objective ("This study investigates...") Methods: - Past: What you did ("Cells were cultured...") - Past: ("We cultured cells...") Results: - Past: Your findings ("Expression increased...") - Past: ("We observed increased expression...") Discussion: - Past: Your results ("Our data showed...") - Present: Established facts ("This gene regulates...") - Present: Interpretations ("These results suggest...") Conclusions: - Present: General conclusions ("This approach provides...") ### Voice by Field Biology/Medicine: - More passive acceptable in methods - Either active or passive in other sections Engineering/Computer Science: - Active voice preferred throughout - "We designed..." rather than "A design was created..." Physics/Chemistry: - Varies by journal and author preference - Either acceptable if consistent ## Quick Reference - Common Issues Results vs Discussion: Keep observations in results, interpretations in discussion Citation Consistency: Use one style throughout (numbered [1] or author-year) Figure References: Reference all figures/tables in text with findings, not just "see Figure X" Statistical Reporting: Include test statistic, df, exact p-value, effect size, variability measure Methods Detail: Include manufacturer, catalog #, concentrations for reproducibility Limitations: Be honest but not self-defeating; explain impact, suggest solutions See individual reference files for detailed examples and guidance. ## Tools and Utilities ### Citation Checker ```bash python scripts/citation_checker.py manuscript.docx --style apa ``` Validates citation consistency between in-text and reference list. ### Figure Generator ```bash python scripts/figure_generator.py data.csv config.yaml --output fig1.pdf ``` Creates publication-quality figures from data. ### Word Counter ```bash python scripts/word_counter.py manuscript.docx ``` Counts words by section for length requirements. ### Readability Analyzer ```bash python scripts/readability_analyzer.py section.txt ``` Analyzes text complexity and suggests improvements. ### Table Formatter ```bash python scripts/table_formatter.py data.csv --format latex --journal nature ``` Formats tables for specific journals. ## Templates Access templates for common document types: - assets/templates/manuscript_template.docx - Generic manuscript - assets/templates/imrad_template.md - IMRAD structure - assets/templates/grant_aims_template.docx - NIH Specific Aims - assets/templates/response_letter_template.docx - Revision response - assets/templates/abstract_template.txt - Structured abstract - assets/templates/methods_checklist.md - Reproducibility checklist ## Style Guides Journal-specific quick references: - assets/style-guides/apa_guide.md - APA style - assets/style-guides/nature_guide.md - Nature requirements - assets/style-guides/science_guide.md - Science requirements - assets/style-guides/cell_guide.md - Cell requirements - assets/style-guides/plos_guide.md - PLOS requirements - assets/style-guides/nih_guide.md - NIH grant guidelines - assets/style-guides/nsf_guide.md - NSF grant guidelines --- > Converted and distributed by [TomeVault](https://tomevault.io/claim/jkitchin) — claim your Tome and manage your conversions.