/scientific-writing

name: scientific-writing
description: "Use when writing or revising scientific manuscript prose: IMRAD sections, abstracts, figure/table captions, citation-integrated paragraphs, reporting-guideline language, terminology, clarity, and journal-submission text."
allowed-tools: [Read, Write, Edit, Bash]

Scientific Writing

Overview

Scientific writing is a process for communicating research with precision and clarity. Write manuscripts using IMRAD structure, citation-integrated prose, figure/table captions, and reporting guidelines (CONSORT/STROBE/PRISMA). Apply this skill for research papers and journal submissions.

**Critical Principle: Always write in full paragraphs with flowing prose. Never submit bullet points in the final manuscript.** Use a two-stage process: first create section outlines with key points, then convert those outlines into complete paragraphs.

When to Use This Skill

This skill should be used when:

• Writing or revising any section of a scientific manuscript (abstract, introduction, methods, results, discussion)
• Structuring a research paper using IMRAD or other standard formats
• Formatting citations and references in specific styles (APA, AMA, Vancouver, Chicago, IEEE)
• Writing figure/table callouts, captions, and result interpretation in manuscript prose
• Applying study-specific reporting guidelines (CONSORT for trials, STROBE for observational studies, PRISMA for reviews)
• Drafting abstracts that meet journal requirements (structured or unstructured)
• Preparing manuscripts for submission to specific journals
• Improving writing clarity, conciseness, and precision
• Ensuring proper use of field-specific terminology and nomenclature
• Revising manuscript prose in response to reviewer comments

Figure And Table Prose Boundary

This skill can specify where figures/tables belong, write captions, and connect display items to the narrative. It does not generate diagrams, plots, posters, or visual assets, and it must not require a separate visual specialist as part of normal writing.

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Core Capabilities

1. Manuscript Structure and Organization

**IMRAD Format**: Guide papers through the standard Introduction, Methods, Results, And Discussion structure used across most scientific disciplines. This includes:

• **Introduction**: Establish research context, identify gaps, state objectives
• **Methods**: Detail study design, populations, procedures, and analysis approaches
• **Results**: Present findings objectively without interpretation
• **Discussion**: Interpret results, acknowledge limitations, propose future directions

For detailed guidance on IMRAD structure, refer to `references/imrad_structure.md`.

**Alternative Structures**: Support discipline-specific formats including:

• Review articles (narrative, systematic, scoping)
• Case reports and case series
• Meta-analyses and pooled analyses
• Theoretical/modeling papers
• Methods papers and protocols

2. Section-Specific Writing Guidance

**Abstract Composition**: Craft concise, standalone summaries (100-250 words) that capture the paper's purpose, methods, results, and conclusions. Support both structured abstracts (with labeled sections) and unstructured single-paragraph formats.

**Introduction Development**: Build compelling introductions that:

• Establish the research problem's importance
• Review relevant literature systematically
• Identify knowledge gaps or controversies
• State clear research questions or hypotheses
• Explain the study's novelty and significance

**Methods Documentation**: Ensure reproducibility through:

• Detailed participant/sample descriptions
• Clear procedural documentation
• Statistical methods with justification
• Equipment and materials specifications
• Ethical approval and consent statements

**Results Presentation**: Present findings with:

• Logical flow from primary to secondary outcomes
• Integration with figures and tables
• Statistical significance with effect sizes
• Objective reporting without interpretation

**Discussion Construction**: Synthesize findings by:

• Relating results to research questions
• Comparing with existing literature
• Acknowledging limitations honestly
• Proposing mechanistic explanations
• Suggesting practical implications and future research

3. Citation-Integrated Prose

Apply citation styles correctly across disciplines. This skill handles citation placement and style in prose; it does not manage reference libraries or bibliography cleanup. For style details, refer to `references/citation_styles.md`.

**Major Citation Styles:**

• **AMA (American Medical Association)**: Numbered superscript citations, common in medicine
• **Vancouver**: Numbered citations in square brackets, biomedical standard
• **APA (American Psychological Association)**: Author-date in-text citations, common in social sciences
• **Chicago**: Notes-bibliography or author-date, humanities and sciences
• **IEEE**: Numbered square brackets, engineering and computer science

**Best Practices:**

• Cite primary sources when possible
• Include recent literature (last 5-10 years for active fields)
• Balance citation distribution across introduction and discussion
• Verify all citations against original sources
• Keep bibliography management as a separate deliverable if the user explicitly asks for it

4. Figure And Table Writing

Write effective figure/table references and captions that enhance comprehension. For detailed best practices, refer to `references/figures_tables.md`.

**When to Use Tables vs. Figures:**

• **Tables**: Precise numerical data, complex datasets, multiple variables requiring exact values
• **Figures**: Trends, patterns, relationships, comparisons best understood visually

**Design Principles:**

• Make each table/figure self-explanatory with complete captions
• Use consistent formatting and terminology across all display items
• Label all axes, columns, and rows with units
• Include sample sizes (n) and statistical anno