/scientific-writing

name: scientific-writing
description: "Write scientific journal manuscripts in full paragraphs (never bullet points). Use a two-stage process: (1) create section outlines with key points from the literature you have gathered, (2) convert to flowing prose. IMRAD structure, citations (APA/AMA/Vancouver), figures/tables, reporting guidelines (CONSORT/STROBE/PRISMA), for research papers and journal submissions."
allowed-tools: [Read, Write, Edit, Bash]

Scientific Writing

Overview

Every claim in the manuscript should be backed by literature you have actually read. Gather it first (the project's `Survey/` files, or a literature skill such as inno-deep-research or academic-researcher), and verify citations before submission (inno-reference-audit).

Scientific writing is a process for communicating research with precision and clarity. Write manuscripts using IMRAD structure, citations (APA/AMA/Vancouver), figures/tables, 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 from the gathered literature, 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)
• Creating, formatting, or improving figures, tables, and data visualizations
• 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
• Addressing reviewer comments and revising manuscripts

Figures

Plan figures early: most papers need a study-design or method overview and one figure per main result. Use `references/figures_tables.md` for design rules. Make data plots from the actual results (matplotlib or similar), and draw diagrams with whatever diagram or figure skill is enabled in the project. Never invent data for a figure.

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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 and Reference Management

Apply citation styles correctly across disciplines. For comprehensive style guides, 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
• Use reference management software (Zotero, Mendeley, EndNote)

4. Figures and Tables

Create effective data visualizations 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

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