scientific-writing — quality + safety report

---
name: scientific-writing
description: Core skill for the deep research and writing tool. Write scientific manuscripts in full paragraphs (never bullet points). Use two-stage process with (1) section outlines with key points using research-lookup then (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
license: MIT license
metadata:
  version: "1.0"
  skill-author: K-Dense Inc.
---

# Scientific Writing

## Overview

**This is the core skill for the deep research and writing tool**—combining AI-driven deep research with well-formatted written outputs. Every document produced is backed by comprehensive literature search and verified citations through the research-lookup skill.

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 using research-lookup, 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

## Visual Enhancement with Scientific Schematics

**⚠️ MANDATORY: Every scientific paper MUST include a graphical abstract plus 1-2 additional AI-generated figures using the scientific-schematics skill.**

This is not optional. Scientific papers without visual elements are incomplete. Before finalizing any document:
1. **ALWAYS generate a graphical abstract** as the first visual element
2. Generate at minimum ONE additional schematic or diagram using scientific-schematics
3. Prefer 3-4 total figures for comprehensive papers (graphical abstract + methods flowchart + results visualization + conceptual diagram)

### Graphical Abstract (REQUIRED)

**Every scientific writeup MUST include a graphical abstract.** This is a visual summary of your paper that:
- Appears before or immediately after the text abstract
- Captures the entire paper's key message in one image
- Is suitable for journal table of contents display
- Uses landscape orientation (typically 1200x600px)

**Generate the graphical abstract FIRST:**
```bash
python scripts/generate_schematic.py "Graphical abstract for [paper title]: [brief description showing workflow from input → methods → key findings → conclusions]" -o figures/graphical_abstract.png
```

**Graphical Abstract Requirements:**
- **Content**: Visual summary showing workflow, key methods, main findings, and conclusions
- **Style**: Clean, professional, suitable for journal TOC
- **Elements**: Include 3-5 key steps/concepts with connecting arrows or flow
- **Text**: Minimal labels, large readable fonts
- Log: `[HH:MM:SS] GENERATED: Graphical abstract for paper summary`

### Additional Figures (GENERATE EXTENSIVELY)

**⚠️ CRITICAL: Use BOTH scientific-schematics AND generate-image EXTENSIVELY throughout all documents.**

Every document should be richly illustrated. Generate figures liberally - when in doubt, add a visual.

**MINIMUM Figure Requirements:**

| Document Type | Minimum | Recommended |
|--------------|---------|-------------|
| Research Papers | 5 | 6-8 |
| Literature Reviews | 4 | 5-7 |
| Market Research | 20 | 25-30 |
| Presentations | 1/slide | 1-2/slide |
| Posters | 6 | 8-10 |
| Grants | 4 | 5-7 |
| Clinical Reports | 3 | 4-6 |

**Use scientific-schematics EXTENSIVELY for technical diagrams:**
```bash
python scripts/generate_schematic.py "your diagram description" -o figures/output.png
```

- Study design and methodology flowcharts (CONSORT, PRISMA, STROBE)
- Conceptual framework diagrams
- Experimental workflow illustrations
- Data analysis pipeline diagrams
- Biological pathway or mechanism diagrams
- System architecture visualizations
- Neural network architectures
- Decision trees, algorithm flowcharts
- Comparison matrices, timeline diagrams
- Any technical concept that benefits from schematic visualization

**Use generate-image EXTENSIVELY for visual content:**
```bash
python scripts/generate_image.py "your image description" -o figures/output.png
```

- Photorealistic illustrations of concepts
- Medical/anatomical illustrations
- Environmental/ecological scenes
- Equipment and lab setup visualizations
- Artistic visualizations, infographics
- Cover images, header graphics
- Product mockups, prototype visualizations
- Any visual that enhances understanding or engagement

The AI will automatically:
- Create publication-quality images with proper formatting
- Review and refine through multiple iterations
- Ensure accessibility (colorblind-friendly, high contrast)
- Save outputs in the figures/ directory

**When in Doubt, Generate a Figure:**
- Complex concept → generate a schematic
- Data discussion → generate a visualization
- Process description → generate a flowchart
- Comparison → generate a comparison diagram
- Reader benefit → generate a visual

For detailed guidance, refer to the scientific-schematics and generate-image skill documentation.

---

## 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**: Diagnostic accuracy studies
- **TRIPOD**: Prediction model studies
- **ARRIVE**: Animal research
- **CARE**: Case reports
- **SQUIRE**: Quality improvement studies
- **SPIRIT**: Study protocols for clinical trials
- **CHEERS**: Economic evaluations

Each guideline provides checklists ensuring all critical methodological elements are reported.

### 6. Writing Principles and Style

Apply fundamental scientific writing principles. For detailed guidance, refer to `references/writing_principles.md`.

**Clarity**:
- Use precise, unambiguous language
- Define technical terms and abbreviations at first use
- Maintain logical flow within and between paragraphs
- Use active voice when appropriate for clarity

**Conciseness**:
- Eliminate redundant words and phrases
- Favor shorter sentences (15-20 words average)
- Remove unnecessary qualifiers
- Respect word limits strictly

**Accuracy**:
- Report exact values with appropriate precision
- Use consistent terminology throughout
- Distinguish between observations and interpretations
- Acknowledge uncertainty appropriately

**Objectivity**:
- Present results without bias
- Avoid overstating findings or implications
- Acknowledge conflicting evidence
- Maintain professional, neutral tone

### 7. Writing Process: From Outline t

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