BioRouter Skills

A collection of skills for BioRouter — UCSF's local-first AI workspace for biomedical research.

Skills are reusable instruction bundles that BioRouter loads on demand to shape how the model writes code, drafts documents, and reasons about a problem. Some run automatically when relevant files are touched (style enforcement, language conventions). Others are user-invocable and respond to a slash command like /ralph or /anti-ai-writing in the chat panel.

This repository hosts the skills curated by the Baranzini Lab at UCSF. Each top-level folder is a single skill (or, for superpowers/, a bundled collection of sub-skills).

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Installing a skill

1. Download the skill's .zip from the Releases page.
2. Unzip it.
3. Move the resulting folder into ~/.config/biorouter/skills/.
4. Open BioRouter. The skill appears under Skills automatically. User-invocable skills respond to /skill-name.

You can also clone individual folders directly into ~/.config/biorouter/skills/ if you prefer to track updates with git.

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Skills in this repo

Skill	Trigger	What it does
anti-ai-writing	/anti-ai-writing	Pass/fail checklist that strips AI tells out of prose, articles, and essays.
develop-biorouter-extension	/develop-biorouter-extension	Step-by-step guide for building a .brxt extension — manifest, MCP server, bundled skills.
ggplot-visualization	Auto (R plotting)	Applies the lab's ggplot2 style automatically whenever R plotting code is written.
python-scripting	Auto (Python)	Enforces Python naming, typing, error handling, and project-structure conventions.
r-scripting	Auto (R)	Tidyverse conventions and documentation standards for R.
ralph	/ralph	End-to-end planning for the Ralph autonomous agent loop — generates a markdown PRD from a feature idea, then converts it to prd.json sized for one-story-per-iteration execution.
superpowers	Mixed (see folder)	A bundled collection of 13 engineering-discipline skills (brainstorming, TDD, systematic debugging, parallel agents, plan writing, code review, git worktrees, more).

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Repository layout

biorouter-skills/
├── anti-ai-writing/
│   └── SKILL.md
├── develop-biorouter-extension/
│   └── SKILL.md
├── ggplot-visualization/
│   └── SKILL.md
├── python-scripting/
│   └── SKILL.md
├── r-scripting/
│   └── SKILL.md
├── ralph/
│   ├── SKILL.md                  ← the skill itself
│   ├── agent-instructions.md     ← prompt for the autonomous loop
│   └── prd.json.example
└── superpowers/
    ├── brainstorming/
    ├── test-driven-development/
    ├── systematic-debugging/
    └── … (10 more)

Every skill folder contains a SKILL.md with YAML frontmatter (name, description, optional user-invocable). Anything else in the folder is supporting material the skill can reference.

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Contributing a new skill

1. Fork this repo.

2. Add a new top-level folder named after your skill (kebab-case).

3. Drop a SKILL.md into it with frontmatter:

   ---
   name: my-skill
   description: One sentence — what it does and when to use it. This is the line the model reads to decide whether to load the skill.
   user-invocable: true   # optional
   ---
   
   # My Skill
   
   The skill body. Be concrete, give examples, and keep it focused on one job.

4. Open a pull request. A maintainer will review and cut a release with a matching .zip so BAAM picks it up automatically.

A good description: is the single most important line — it is what the model sees when deciding whether to invoke the skill, so be specific about when to use it, not just what it does.

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License & attribution

Skills here are licensed under Apache 2.0, matching the BioRouter project. Some skills (the superpowers/ collection, anti-ai-writing) are adapted from upstream open-source skill libraries; see each skill's frontmatter for attribution where applicable.

Maintained by the Baranzini Lab at UCSF.