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 at least 1-2 AI-generated figures using the scientific-schematics skill.
This is not optional. Scientific papers without visual elements are incomplete. Before finalizing any document:
- Generate at minimum ONE schematic or diagram using scientific-schematics
- Prefer 2-3 figures for comprehensive papers (methods flowchart, results visualization, conceptual diagram)
How to generate figures:
- Use the scientific-schematics skill to generate AI-powered publication-quality diagrams
- Simply describe your desired diagram in natural language
- Nano Banana Pro will automatically generate, review, and refine the schematic
How to generate schematics:
python scripts/generate_schematic.py "your diagram description" -o figures/output.png
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 to add schematics:
- 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
- Any complex concept that benefits from visualization
For detailed guidance on creating schematics, refer to the scientific-schematics 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 improve