/scientific-writing

id: scientific-writing
name: scientific-writing
version: 1.0.0
description: |-
  Core skill for the deep research and writing tool.
stages: ["publication"]
tools: ["read_file", "search_project", "write_file"]
summary: |-
  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 pros...
primaryIntent: writing
intents: ["writing", "research"]
capabilities: ["visualization-reporting"]
domains: ["general"]
keywords: ["scientific-writing", "paper writing", "visualization-reporting", "scientific", "writing", "core", "deep", "research", "tool", "write", "manuscripts", "full"]
source: builtin
status: verified
upstream:
  repo: dr-claw
  path: skills/scientific-writing
  revision: 8322dc4ef575affaa374aa7922c0a0971c6db7d7
resourceFlags:
  hasReferences: true
  hasScripts: false
  hasTemplates: false
  hasAssets: false
  referenceCount: 5
  scriptCount: 0
  templateCount: 0
  assetCount: 0
  optionalScripts: false

scientific-writing

Canonical Summary

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 pros...

Trigger Rules

Use this skill when the user request matches its research workflow scope. Prefer the bundled resources instead of recreating templates or reference material. Keep outputs traceable to project files, citations, scripts, or upstream evidence.

Resource Use Rules

• Read from `references/` only when the current task needs the extra detail.

Execution Contract

• Resolve every relative path from this skill directory first.
• Prefer inspection before mutation when invoking bundled scripts.
• If a required runtime, CLI, credential, or API is unavailable, explain the blocker and continue with the best manual fallback instead of silently skipping the step.
• Do not write generated artifacts back into the skill directory; save them inside the active project workspace.

Upstream Instructions

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, acknowl