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gaspolymerase/biomanager

v1.3.0MIT

Tell your assistant what you did in the lab, in your words or with a photo of your notes; it proposes the records in your lab's BioManager, and you approve them there.

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BioManager for AI assistants

BioManager keeps a lab's animals, stocks and supplies in one place: mice, zebrafish, flies, worms, plasmids, samples, reagents, experiments and a lab notebook. It is open source, and each lab runs its own, on a desktop or on a lab server.

This plugin lets your assistant (Claude, ChatGPT and Codex, Cursor, VS Code with GitHub Copilot, and others that read skills) work with your lab's BioManager. Tell it what you did, in your own words or with a photo of your notebook, whiteboard or cage cards:

Litter in cage 102 yesterday, 7 pups; moved the two old breeders from 88 to 91; injected day 3 of the TMX cohort this morning.

It looks up each cage, mouse and experiment you mention, asks you when something could be more than one record, and sends one proposal. You read it in BioManager and press Approve, which makes every change at once as one batch you can undo, or Discard. The assistant never changes anything itself.

Once the plugin is added, you don't need to explain anything first: "I want to change something in BioManager" is enough, and it shows you what's due today and asks what you did.

What it adds

  • A skill that teaches the assistant how to work with BioManager: look up every record, never guess, send everything as one proposal, give you the link.
  • Nine commands: Log today's work from my notes, Log from a photo of my notebook, whiteboard or cage card, Turn my captures from the bench into records, Plan tomorrow from what's due, Review the lab this week, Design an experiment, Write the methods for an experiment, Draft the animal-use report for an annual review and Write a handover for someone leaving the lab. The numbers in them (animals available, breeding odds, animals per group, group allocation, animals used per protocol) are worked out by BioManager, not by the assistant.
  • The connection to your BioManager, in Claude Code: it asks for your BioManager's MCP address when the plugin is enabled.

Connect your BioManager

Each lab's BioManager has its own address, shown in BioManager under Help → Connect an AI assistant.

  • Claude on the web, the desktop app or a phone: after adding the plugin, add BioManager as a custom connector (Settings → Connectors → Add custom connector) with that address, and sign in with a connection code from the same page. This needs your lab's server to be on the internet. On a Team or Enterprise plan, an owner can add it for the whole lab.
  • Claude Code: enter the address when the plugin asks, then type /mcp, choose biomanager, and press Allow in the browser that opens.
  • ChatGPT (on the web): Plugins → + → Add custom MCP server, with that address. Codex: codex mcp add biomanager --url <address>, then codex mcp login biomanager.
  • Cursor, VS Code and Cherry Studio: the Add to … buttons on BioManager's Connect page.

The AI assistants guide has the details, including the BioManager desktop app and servers that are only on the lab network.

Privacy

The plugin itself collects nothing and sends nothing anywhere. It is instructions for the assistant, plus, in Claude Code, the address of your own BioManager. When you use it, the assistant reads your lab's records from your BioManager, as you and with your permissions, and sends proposals back to it. What the assistant sees is handled under your agreement with the company that makes it (Anthropic for Claude, OpenAI for ChatGPT and Codex). BioManager's makers never see your records. Revoke the connection at any time under Settings → AI assistant & tokens in BioManager. The full policy is at biomanager.org/privacy, and the terms at biomanager.org/terms.

Licence

MIT, like BioManager. Source and issues: github.com/gaspolymerase/biomanager.