Scientific Writing
Write clear, precise, and publication-ready scientific manuscripts.
When to Use
- Drafting manuscript sections (abstract, intro, methods, results, discussion)
- Structuring a research paper using IMRAD format
- Formatting citations and references
- Creating or improving figures and tables
- Applying reporting guidelines (CONSORT, STROBE, PRISMA)
- Preparing manuscripts for journal submission
- During the WRITING or REVIEW phases
Manuscript Structure (IMRAD)
┌─────────────────────────────────────────────────────────────┐
│ TITLE │
│ Concise, specific, informative (12-15 words) │
├─────────────────────────────────────────────────────────────┤
│ ABSTRACT (150-250 words) │
│ Background → Objective → Methods → Results → Conclusion │
├─────────────────────────────────────────────────────────────┤
│ INTRODUCTION │
│ Context → Gap → Objective → Approach │
│ Funnel: Broad → Narrow → Your question │
├─────────────────────────────────────────────────────────────┤
│ METHODS │
│ Study design → Participants → Procedures → Analysis │
│ Enough detail for replication │
├─────────────────────────────────────────────────────────────┤
│ RESULTS │
│ Objective findings, no interpretation │
│ Text + Figures + Tables │
├─────────────────────────────────────────────────────────────┤
│ DISCUSSION │
│ Key findings → Context → Limitations → Implications │
│ Reverse funnel: Specific → Broad │
├─────────────────────────────────────────────────────────────┤
│ REFERENCES │
│ Consistent style, verified DOIs │
└─────────────────────────────────────────────────────────────┘
Section-by-Section Guidance
Abstract
Purpose: Standalone summary of the entire paper
Structure (for structured abstracts):
- Background: Why this matters (1-2 sentences)
- Objective: What you did (1 sentence)
- Methods: How you did it (2-3 sentences)
- Results: Key findings with numbers (3-4 sentences)
- Conclusion: Main takeaway (1-2 sentences)
Tips:
- Write LAST after all other sections
- Include specific numbers/results
- Avoid abbreviations (or define them)
- Stay within word limit (usually 150-250)
Introduction
Purpose: Establish context, gap, and rationale
Structure (Funnel):
- Broad context (1-2 paragraphs): Why does this field matter?
- Current knowledge (2-3 paragraphs): What's known? What approaches exist?
- Gap/Problem (1 paragraph): What's missing? What's the controversy?
- Your study (1 paragraph): What did you do? Why this approach?
Tips:
- End with clear objectives or hypotheses
- Cite 20-40 references typically
- Use present tense for established facts
- Be specific about what you're studying
Methods
Purpose: Enable replication
Key Sections:
- Study Design: Type of study, setting, dates
- Participants/Samples: Selection, criteria, sample size, ethics
- Procedures: What was done, in order
- Measurements: What and how measured
- Statistical Analysis: Tests, software, significance criteria
Common Mistakes: | Mistake | Problem | Fix | |---------|---------|-----| | Vague methods | "Standard methods" | Specify exact protocol | | Missing stats | "Data were analyzed" | Name specific tests | | No software versions | Not reproducible | Include version numbers | | Missing sample size justification | Why this n? | Add power analysis |
Tips:
- Use past tense
- Be specific: model numbers, concentrations, durations
- Reference published protocols if applicable
- Include ethical approvals
Results
Purpose: Present findings objectively
Organization:
- Order by importance or by methods flow
- Each paragraph: finding + evidence (figure/table reference)
- Stats: test, statistic, df, p-value, effect size
Structure Pattern:
[What was found] (Figure X).
[Statistical support] (t(df) = X.XX, p = .XXX, d = X.XX).
[Additional detail or subgroup analysis].
Tips:
- NO interpretation (save for Discussion)
- Include negative/null results
- Reference every figure and table
- Use past tense
- Include exact p-values (not just p < 0.05)
Discussion
Purpose: Interpret findings in context
Structure (Reverse Funnel):
- Key findings (1-2 paragraphs): Main results, directly address objectives
- Comparison to literature (2-3 paragraphs): How do findings fit with prior work?
- Mechanisms (1-2 paragraphs): Why might this happen?
- Limitations (1 paragraph): Be honest and specific
- Implications (1-2 paragraphs): Clinical, practical, theoretical significance
- Future directions (optional): What next?
- Conclusion (1 paragraph): Main takeaway
Tips:
- Start with your results, not literature
- Acknowledge limitations honestly
- Don't overstate conclusions
- Distinguish correlation from causation
Citation Styles
APA (7th Edition)
In-text: (Author, Year) or Author (Year)
Previous research found significant effects (Smith, 2023).
Smith (2023) reported significant effects.
Reference list:
Smith, J. D., Johnson, M. L., & Williams, K. R. (2023). Title of
article. Journal Name, 22(4), 301-318. https://doi.org/10.xxx/yyy
Vancouver/ICMJE
In-text: Superscript or bracketed numbers¹ or [1]
Previous research found significant effects.¹
Multiple studies support this finding.¹⁻³
Reference list (numbered):
1. Smith JD, Johnson ML, Williams KR. Title of article. J Name.
2023;22(4):301-18.
Nature
In-text: Superscript numbers¹
Previous research found significant effects¹.
Reference list:
1. Smith, J. D., Johnson, M. L. & Williams, K. R. Title of article.
Nat. Rev. Drug Discov. 22, 301-318 (2023).
Figures and Tables
When to Use Which
| Use Tables For | Use Figures For | |----------------|-----------------| | Exact values needed | Trends and patterns | | Many variables | Comparisons | | Summary statistics | Relationships | | Participant characteristics | Processes |
Figure Checklist
- [ ] Self-explanatory with caption
- [ ] Axes labeled with units
- [ ] Error bars defined (SEM, SD, CI)
- [ ] Significance markers explained
- [ ] Colorblind-safe
- [ ] Resolution ≥300 DPI
Table Checklist
- [ ] Clear, descriptive title
- [ ] Column headers with units
- [ ] Appropriate precision (not too many decimals)
- [ ] Notes for abbreviations
- [ ] n values included
Caption Template
**Figure 1. Brief descriptive title.**
(A) Description of panel A. (B) Description of panel B.
Data shown as mean ± SEM (n = X per group). Statistical
comparisons by [test name]. *p < 0.05, **p < 0.01, ***p < 0.001.
Reporting Guidelines
Which Guideline to Use
| Study Type | Guideline | URL | |------------|-----------|-----| | Randomized trial | CONSORT | consort-statement.org | | Observational (cohort, case-control) | STROBE | strobe-statement.org | | Systematic review | PRISMA | prisma-statement.org | | Diagnostic accuracy | STARD | stard-statement.org | | Prediction models | TRIPOD | tripod-statement.org | | Animal research | ARRIVE | arriveguidelines.org | | Case reports | CARE | care-statement.org | | Quality improvement | SQUIRE | squire-statement.org |
Using Checklists
- Download checklist from guideline website
- Complete each item during writing
- Include page/line numbers
- Submit with manuscript (often required)
Writing Principles
Clarity
- Use precise, unambiguous language
- One idea per sentence
- Define technical terms at first use
- Use active voice when possible
Example:
❌ "The samples were subjected to analysis"
✓ "We analyzed the samples using..."
❌ "It has been shown that..."
✓ "Smith et al. (2023) showed that..."
Conciseness
| Wordy | Concise | |-------|---------| | "Due to the fact that" | "Because" | | "In order to" | "To" | | "A large number of" | "Many" | | "At the present time" | "Now" / "Currently" | | "In the event that" | "If" | | "Has the ability to" | "Can" |
Accuracy
- Report exact values with appropriate precision
- Use consistent terminology
- Distinguish observation from interpretation
- Acknowledge uncertainty
Objectivity
- Present results without bias
- Don't overstate findings
- Acknowledge contradictory evidence
- Maintain professional, neutral tone
Field-Specific Terminology
General Principles
- Match terminology to the target journal
- Use established nomenclature systems
- Define abbreviations at first use
- Be consistent throughout
Quick Reference
| Field | Convention | |-------|------------| | Genes | Italics (BRCA1) | | Proteins | Roman (BRCA1) | | Species | Italics, full at first (Escherichia coli), then abbreviated (E. coli) | | Statistics | Italics (p, n, t, F, r) | | Drugs | Generic name first, brand in parentheses |
Common Mistakes to Avoid
Top Rejection Reasons
- Incomplete or inappropriate statistics
- Over-interpretation of results
- Poor methods description
- Inadequate sample size
- Poor writing quality
- Inadequate literature review
- Unclear figures
- Failure to follow guidelines
Writing Issues
| Issue | Example | Fix | |-------|---------|-----| | Tense mixing | "We collected... and analyze" | Past for methods/results | | Excessive jargon | Too many undefined terms | Define or simplify | | Paragraph breaks | Random breaks | One topic per paragraph | | Missing transitions | Abrupt section changes | Add linking sentences |
Manuscript Development Workflow
Recommended Order
- Figures/Tables first (core data story)
- Methods (often easiest to draft)
- Results (describe figures/tables)
- Discussion (interpret findings)
- Introduction (set up the question)
- Abstract (synthesize everything)
- Title (last refinement)
Revision Checklist
- [ ] Logical flow throughout
- [ ] Consistent terminology
- [ ] All figures/tables referenced
- [ ] All citations verified
- [ ] Word counts met
- [ ] Reporting checklist complete
- [ ] Journal format requirements met
Integration with RA Workflow
WRITING Phase Files
| File | Purpose |
|------|---------|
| manuscript/background.md | Introduction content |
| manuscript/methods.md | Methods section |
| manuscript/results.md | Results + figure refs |
| manuscript/discussion.md | Discussion section |
| manuscript/figures/figN/caption.md | Figure captions |
Connected Skills
- ←
/write_background: Drafts introduction - ←
/write_methods: Generates methods from scripts - ←
/write_results: Drafts results from figures - →
/peer_review: Self-review before submission