ClawBio Documentation
Run real genomics with an AI agent in about ten minutes. No coding experience needed.
Start here¶
This is for a biologist who has never opened a terminal. You will install one AI agent, then let the agent install ClawBio and run your first analysis for you. Budget ten minutes.
What is an AI agent?
A chatbot answers questions. An agent also does things on your computer: it can install software, run programs and read the files they produce. You will type plain English and the agent will do the terminal work. Two good agents are Claude Code (Anthropic) and Codex (OpenAI). Pick whichever company you already have a paid account with; the free tiers do not include these agents.
Step 1. Open a terminal¶
The terminal is the text window agents live in. You only need it to run three commands.
Press Cmd+Space, type Terminal, press Enter.
Press the Windows key, type PowerShell, press Enter. Your prompt starts with PS C:\.
Press Ctrl+Alt+T, or open Terminal from your applications menu.
Step 2. Install an agent¶
Copy one line, paste it into the terminal, press Enter, and wait for it to finish.
Needs a Claude Pro, Max, Team or Enterprise account (claude.ai).
Mac and Linux
Windows (PowerShell)
Close the terminal, open a new one, and check it worked:
Prefer clicking to typing? The Claude Code desktop app does the same job without a terminal.
Needs a ChatGPT Plus, Pro, Business or Enterprise account (chatgpt.com).
Mac and Linux
Windows (PowerShell), or any machine that already has Node.js
Close the terminal, open a new one, and check it worked:
Step 3. Make a folder and start the agent in it¶
Agents work inside one folder at a time. Make an empty one for your genomics work and start the agent there. The first start opens your browser to sign in; say yes.
Step 4. Paste this prompt¶
Copy the whole block into the agent and press Enter. The agent installs Python if you do not have it, installs ClawBio, runs a pharmacogenomics report on bundled demo data, and explains the result. Approve each action it proposes.
I am a biologist with no programming experience. Please set up ClawBio for me
and run its first demo, explaining what you are doing in plain language.
1. Check whether Python 3.11 or newer is installed. If it is not, install it
for my operating system and confirm it works.
2. Install ClawBio with: pip install clawbio
3. Run: clawbio run pharmgx --demo
4. Open the report it produces and explain the findings to me as you would to
a colleague: which genes were tested, what each result means, and what the
reproducibility bundle is for.
5. Then run: clawbio list
and tell me which three skills you think I should try next and why.
Step 5. What you should see¶
In under two seconds after install, the PharmGx demo writes a report with CYP2D6, CYP2C19 and other drug-metabolism gene calls, a Markdown summary, and a reproducibility/ folder holding the exact commands, environment and SHA-256 checksums. The agent will walk you through it. From here you can ask it anything in English: "run the GWAS PRS demo", "explain what a polygenic score is before you run it", "which of these skills works on my own 23andMe file".
Where the skills live
Once ClawBio is installed, both agents can already run every skill through the clawbio command. Claude Code users can also load the skills as a plugin so the agent knows when to use each one without being told: type /plugin marketplace add ClawBio/ClawBio and then /plugin install clawbio inside Claude Code. Codex, Cursor and other editors that read Agent Skills folders can copy any skill from skills/ in the repository into ~/.agents/skills/.
Next: Step 1 of the ClawBio tutorial series picks up from exactly this point.
Quick install (already have Python?)¶
Prefer conda? conda install -c bioconda clawbio.
Using Claude Code? Install the skills as a plugin:
Developing ClawBio, or want every skill with its full demo data? Work from a source checkout instead (uv recommended):
git clone https://github.com/ClawBio/ClawBio.git && cd ClawBio
uv sync
uv run python clawbio.py run pharmgx --demo
Explore
Try Conversational Genome
Ask questions about a public genome in a hosted chat. No notebook setup. Includes live skill execution and precomputed findings, with limitations explained.
ClawBio + Nebius Hackathon Berlin
One day building agents that do real genomics, at Impact Hub Berlin. Free, lunch provided, Nebius credits for the best builds. Setup, tracks and running order.
Setup
Install an AI coding agent, connect it to a model provider, and run your first prompt.
Build a Skill
Write a SKILL.md, add Python implementation, and submit a PR.
Skill Library
Browse all available skills: pharmacogenomics, GWAS, scRNA-seq, equity scoring, and more.
Presentations
All ClawBio talks, workshops, and pitch decks in one place, newest first.
Deployment
Deploy ClawBio via Docker, Railway, or private cloud.
Variant Interpretation Workshop
Annotate a real human genome in Google Colab. No installation, no terminal, no prior experience required.
30x WGS Workshop
Explore a real 30x whole-genome sequence: structural variants, QC metrics, and pharmacogenomics beyond SNP arrays.
Skill Library · SKILL.md Spec · Contributing · All Tutorials · Presentations