• 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: #+begin_src 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 #+end_src

*** 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: #+begin_src bash

Validate citation consistency

python scripts/citation_checker.py manuscript.docx --style apa #+end_src

*** 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: #+begin_src bash

Analyze readability

python scripts/readability_analyzer.py section.txt

Count words by section

python scripts/word_counter.py manuscript.docx #+end_src

*** 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

#+begin_src bash python scripts/citation_checker.py manuscript.docx --style apa #+end_src

Validates citation consistency between in-text and reference list.

*** Figure Generator

#+begin_src bash python scripts/figure_generator.py data.csv config.yaml --output fig1.pdf #+end_src

Creates publication-quality figures from data.

*** Word Counter

#+begin_src bash python scripts/word_counter.py manuscript.docx #+end_src

Counts words by section for length requirements.

*** Readability Analyzer

#+begin_src bash python scripts/readability_analyzer.py section.txt #+end_src

Analyzes text complexity and suggests improvements.

*** Table Formatter

#+begin_src bash python scripts/table_formatter.py data.csv --format latex --journal nature #+end_src

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