/scientific-writing

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: (1) create section outlines with key points using research-lookup, (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

**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: 1. Generate at minimum ONE schematic or diagram using scientific-schematics 2. 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.

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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.