mcpbeat Sign in

Chapter Skeleton Skill for Codex

by WILLOSCAR

| Build a retrieval-informed chapter skeleton (`outline/chapter_skeleton.yml`) from taxonomy/core scope before stable H3 decomposition.

2k tokens
context cost
the whole folder, loaded on every use
4
files
ships runnable scripts
0
copies elsewhere
how many repositories repackaged it
496
stars on the repo
on the repository, not the skill itself

Install

one command, takes just this skill from the repository 
npx skills add https://github.com/WILLOSCAR/research-units-pipeline-skills --skill chapter-skeleton

What comes with it

5 610 bytes besides the instruction
assets/output_contract.json
references/overview.md
scripts/run.py

The instruction itself

10 sections, as written by the author

Chapter Skeleton

Explicit refinement marker

Create outline/chapter_skeleton.refined.ok only after reviewing a manually refined skeleton. A changed taxonomy, goal, or generator invalidates the marker; reruns then back up and rebuild the skeleton.

Load Order

Always read:

  • references/overview.md

Use scripts/run.py only for deterministic materialization:

  • read outline/taxonomy.yml for retrieval-informed topic structure
  • read GOAL.md when present for scope hints
  • emit outline/chapter_skeleton.yml
  • preserve reviewed user work only through the current explicit refinement marker

Inputs

  • outline/taxonomy.yml
  • Optional: GOAL.md

Outputs

  • outline/chapter_skeleton.yml

Asset contract

  • assets/output_contract.json

Script

Quick Start

  • uv run python .codex/skills/chapter-skeleton/scripts/run.py --workspace <workspace>

All Options

  • --workspace <dir>: workspace containing outline/taxonomy.yml
  • --unit-id <id>: optional harness metadata
  • --inputs <semicolon-separated>: optional override from UNITS.csv
  • --outputs <semicolon-separated>: optional output override; default is outline/chapter_skeleton.yml
  • --checkpoint <C*>: optional harness metadata

Examples

  • Generate the chapter skeleton after taxonomy:
  • uv run python .codex/skills/chapter-skeleton/scripts/run.py --workspace <workspace> --inputs 'outline/taxonomy.yml;GOAL.md' --outputs 'outline/chapter_skeleton.yml'

Other skills for the same job

different authors, same section of the catalogue
Protocolsio Integration
by christophacham
×4

Integration with protocols.io API for managing scientific protocols. This skill should be used when working with protocols.io to search, create, update, or publish protocols; manage protocol steps and materials; handle discussions and comments; organize workspaces; upload and manage files; or integrate protocols.io functionality into workflows. Applicable for protocol discovery, collaborative protocol development, experiment tracking, lab protocol management, and scientific documentation.

16k tokens
Tailored Resume Generator
by frostant
×4

Analyzes job descriptions and generates tailored resumes that highlight relevant experience, skills, and achievements to maximize interview chances

3k tokens
Excalidraw Diagram Generator
by github
vendor ×3

Generate Excalidraw diagrams from natural language descriptions. Use when asked to "create a diagram", "make a flowchart", "visualize a process", "draw a system architecture", "create a mind map", or "generate an Excalidraw file". Supports flowcharts, relationship diagrams, mind maps, and system architecture diagrams. Outputs .excalidraw JSON files that can be opened directly in Excalidraw.

36k tokens scripts
Expo Dev Client
by openai
vendor ×3

Build and distribute Expo development clients locally or via TestFlight

961 tokens
Executing Plans
by ZhanlinCui
×3

Use when you have a written implementation plan to execute in a separate session with review checkpoints

542 tokens
Anndata
by christophacham
×3

Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.

16k tokens
Benchling Integration
by christophacham
×3

Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.

14k tokens
Biopython
by christophacham
×3

Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.

24k tokens

How to use it

Copy the folder

Take willoscar/chapter-skeleton from the repository into ~/.claude/skills for personal use, or into .claude/skills inside a project.

Check the name does not clash

The agent identifies a skill by the name field in its header. Two skills with the same name cannot sit side by side — one of them will be ignored.