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, reasons about a problem, and runs research. Some run automatically when relevant files are touched (style enforcement, language conventions, bioinformatics tasks). Others are user-invocable and respond to a slash command like /ralph, /auto-research, 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; a few folders (superpowers/, bio-skills/) are bundled collections of many sub-skills.

---

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 drag a .zip (or a single SKILL.md) onto Skills → Add Skill inside BioRouter, or clone individual folders directly into ~/.config/biorouter/skills/ to track updates with git.

---

Core skills

General-purpose skills — research, writing, planning, code style, and design.

Skill	Trigger	What it does
scientific-research	/scientific-research	End-to-end research pipeline: scope → literature review → hypotheses → analysis plan → verification → cited write-up. Orchestrates bio-skills and the BioRouter extensions; never fabricates citations or results.
anti-ai-writing	/anti-ai-writing	Pass/fail checklist that strips AI tells out of prose, articles, and essays.
taste-skill	Auto (frontend design)	Anti-slop frontend design — landing pages, portfolios, dashboards, and paper companion sites that don't look templated.
develop-biorouter-extension	/develop-biorouter-extension	Step-by-step guide for building a .brxt extension — manifest, MCP server, bundled skills.
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. Adapted from snarktank/ralph (MIT), itself based on Geoffrey Huntley's Ralph pattern.
ucsf-hpc	/ucsf-hpc	SSH setup, SLURM templates (CPU/GPU/H200), file transfer, and module management for the UCSF CHPC cluster.
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.
ggplot-visualization	Auto (R plotting)	Applies the lab's ggplot2 style whenever R plotting code is written.
superpowers	Mixed	A bundled collection of 13 engineering-discipline skills (brainstorming, TDD, systematic debugging, parallel agents, plan writing, code review, git worktrees, more).

---

Developer & authoring skills

Engineering, review, and skill-authoring tools — adapted from Anthropic's official Claude Code plugins (Apache 2.0). Each upstream plugin ships as slash-commands and subagents (none of them carry lifecycle hooks); BioRouter has no commands/ or agents/ loader, so each plugin's commands and subagents are folded into one self-contained SKILL.md the model loads on demand. hookify is the exception — BioRouter has a hook engine, so it writes genuine, enforced hooks in <project>/.biorouter/hooks.yaml instead of honor-system notes.

Skill	Trigger	What it does
code-review	/code-review	Multi-stage, confidence-scored review of a pull request (or local diff); drops low-confidence findings and posts a formatted PR comment via gh.
code-simplifier	/code-simplifier	Simplifies recently-changed code for clarity while preserving exact behavior; defers language style to python-scripting/r-scripting.
commit-commands	/commit-commands	Three git workflows — clean single commit; commit + push + open PR; and clean up [gone] branches and their worktrees.
skill-creator	/skill-creator	The canonical guide to authoring BioRouter skills — frontmatter, progressive disclosure, packaging, and testing.
hookify	/hookify	Captures project guardrails (warn/block rules) and writes them as real Biorouter hooks in <project>/.biorouter/hooks.yaml — a block rule stops the action, a warn rule surfaces a notice. Requires hooks.allow_project_hooks: true.
code-modernization	/code-modernization	Phased legacy-modernization workflow: preflight → assess → map → extract rules → brief → transform → harden → status.
playground	/playground	Generates self-contained single-file interactive HTML playgrounds for configuring something visually and copying out a prompt.
frontend-design	Auto (frontend work)	Anthropic's anti-slop frontend guidance; complements the taste-skill.

---

BioSkills — bioinformatics bundle

bio-skills/ is a large, context-triggered bundle covering the working biologist's toolkit: sequence I/O, alignment, variant calling, single-cell, ATAC/ChIP-seq, proteomics, metabolomics, pathway analysis, machine learning, workflow management, and more — 456 individual skills across 63 categories in this snapshot (upstream now ships 540). These load automatically when BioRouter sees a relevant file or task (a .vcf, a scanpy import, a Seurat object). See bio-skills/INDEX.md for the full catalog.

Integrated from GPTomics/bioSkills (MIT). BioRouter's house style prefers uv over pip; skills with pip install lines carry a one-line uv tip banner while leaving the original commands intact for reproducibility.

scientific-research is designed to delegate to this bundle — and to the SPOKE, CDW, OMOP, and MedCP extensions — for any biomedical data access, so the orchestrator never has to recall facts from memory.

---

Repository layout

biorouter-skills/
├── LICENSE                        ← MIT
├── auto-research/SKILL.md
├── anti-ai-writing/SKILL.md
├── taste-skill/SKILL.md
├── develop-biorouter-extension/SKILL.md
├── ggplot-visualization/SKILL.md
├── python-scripting/SKILL.md
├── r-scripting/SKILL.md
├── ucsf-hpc/SKILL.md
├── ralph/
│   ├── SKILL.md                   ← the skill itself
│   ├── agent-instructions.md      ← prompt for the autonomous loop
│   └── prd.json.example
├── superpowers/                   ← 13 sub-skill collection
│   ├── brainstorming/
│   ├── test-driven-development/
│   └── …
└── bio-skills/                    ← bioinformatics bundle (63 categories)
    ├── INDEX.md
    ├── single-cell/
    ├── variant-calling/
    └── …

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.

---

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.

---

Sources & attribution

This repository is licensed under the MIT License. Most skills are adapted from open-source projects; we keep their original license and credit the upstream author. The table below is the full directory of where each skill comes from and what we changed to fit BioRouter. Lab-original skills are written by the Baranzini Lab.

Skill	Source	License	What changed for BioRouter
bio-skills	GPTomics/bioSkills	MIT	Dropped the bio- name prefix, set user-invocable: false, and added a one-line uv tip banner to skills that shipped pip install commands (originals left intact). 456 skills / 63 categories in this snapshot; upstream has since grown to 540.
taste-skill	Leonxlnx/taste-skill	MIT	Wired to BioRouter's auto-trigger on frontend work; content kept. Attribution header retained in the SKILL.md.
superpowers	obra/superpowers by Jesse Vincent	MIT	Folded the 13 engineering-discipline skills in; dropped the upstream using-superpowers dispatcher and its SessionStart hook (BioRouter discovers skills natively). verification-before-completion and finishing-a-development-branch gained an optional Stop-hook recipe to hard-enforce "tests pass before finishing."
ralph	snarktank/ralph by Ryan Carson, after Geoffrey Huntley's Ralph pattern	MIT	Reworked the PRD → prd.json → one-story-per-iteration flow around BioRouter's agent loop and /ralph invocation.
code-review, code-simplifier, commit-commands, skill-creator, code-modernization, playground, frontend-design	anthropics/claude-plugins-official	Apache 2.0	Each upstream plugin's slash-commands and subagents folded into one SKILL.md (these plugins ship no hooks). Shell routed through the Developer extension; lab-specific defaults adjusted. Each SKILL.md keeps a source header.
hookify	anthropics/claude-plugins-official → hookify	Apache 2.0	Rewritten to generate real, enforced BioRouter hooks (<project>/.biorouter/hooks.yaml) — the upstream's enforced-hook behavior, expressed in BioRouter's native hook schema.
scientific-research	Lab-original	MIT	— Orchestrates bio-skills and the SPOKE / CDW / OMOP / MedCP extensions.
anti-ai-writing	Lab-original	MIT	— Prose checklist for stripping AI tells.
ucsf-hpc	Lab-original	MIT	— UCSF CHPC cluster: SSH, SLURM templates, modules.
python-scripting, r-scripting, ggplot-visualization	Lab-original	MIT	— House style for Python, R, and ggplot2; auto-triggered by file context.
develop-biorouter-extension	Lab-original	MIT	— Guide for the .brxt extension format.

Maintained by the Baranzini Lab at UCSF.