Scientific WritingSAFE

Kosmos: An AI Scientist for Autonomous Discovery - An implementation and adaptation to be driven by Claude Code or API - Based on the Kosmos AI Paper - https://arxiv.org/abs/2511.02824

The instruction file, verbatim from the audited commit — this is the text the model reads, and the surface the audit's instruction layer examines. Quoted here so you can judge it without cloning anything.

---
name: scientific-writing
description: "Write scientific manuscripts. IMRAD structure, citations (APA/AMA/Vancouver), figures/tables, reporting guidelines (CONSORT/STROBE/PRISMA), abstracts, for research papers and journal submissions."
---

# Scientific Writing

## Overview

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.

## 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

## 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
- **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 annotations
- Follow the "one table/figure per 1000 words" guideline
- Avoid duplicating information between text, tables, and figures

**Common Figure Types:**
- Bar graphs: Comparing discrete categories
- Line graphs: Showing trends over time
- Scatterplots: Displaying correlations
- Box plots: Showing distributions and outliers
- Heatmaps: Visualizing matrices and patterns

### 5. Reporting Guidelines by Study Type

Ensure completeness and transparency by following established reporting standards. For comprehensive guideline details, refer to `references/reporting_guidelines.md`.

**Key Guidelines:**
- **CONSORT**: Randomized controlled trials
- **STROBE**: Observational studies (cohort, case-control, cross-sectional)
- **PRISMA**: Systematic reviews and meta-analyses
- **STARD**:

SAFEgrade B · trust 89/100 Nothing in the source contradicts what it says it does. Grade A is reserved for packages that have also passed the behavioural sandbox.

What the source does

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Gates applied: no_behavioural_pass.