Data and help

AI assistants

Tell an AI assistant what you did; it proposes the records, and you approve them in BioManager.

BioManager has no AI inside it. If you already use an assistant (Claude, ChatGPT, Cursor, Cherry Studio or another app that speaks MCP), you can connect it to your lab. Tell it what you did, in your own words or with a photo of your notebook (litter in 102 yesterday, 7 pups; moved the two old breeders from 88 to 91; injected day 3 of the TMX cohort this morning), and it turns that into records: as one proposal, which you approve in BioManager. It never changes anything itself.

Connect an assistant

Open Settings → API tokens → Connect an AI assistant. It shows the ways in for your BioManager, with its address filled in. Nothing needs installing, except for Claude Desktop on the lab network (below).

From claude.ai, the Claude apps or ChatGPT

These apps reach BioManager from the internet, so this works when your lab's server is on the internet: its admin turns on internet access (in the server's runbook). Then the Connect page shows the connector address, ending in /api/v1/mcp. The desktop app can't be reached this way; use the way below.

1. Add BioManager as a custom connector with that address. In Claude: Settings → Connectors → Add custom connector (on a Team or Enterprise plan, an owner adds it first). In ChatGPT: Settings → Connectors, with developer mode on, then create a connector with OAuth.
2. When it asks you to connect, a BioManager page opens asking for a connection code. On the Connect page (on the lab network), press Get a connection code, type it in, and press Allow. A code works once, for 10 minutes.
3. That's it, on the web and in the phone app alike. The connection is listed under Settings → API tokens with the app's name; revoke it there to end it.

From Claude Code, Cursor, Cherry Studio or Claude Desktop

These run on a computer that can reach BioManager: the same computer as the desktop app, or any computer on the lab network for a lab server. No internet access is needed.

1. On the Connect page, press Make a token. It makes a token that may Read and propose, and the next page shows the setup to copy for each app, with the address and the token filled in. Copy it now: the token is shown once.
2. Claude Code: one command in a terminal. Cursor and Cherry Studio: the address and the token, in their MCP settings. Claude Desktop runs a small program from BioManager's source instead, mcp/biomanager_mcp.py (install it once with python -m pip install -r mcp/requirements.txt); the steps are in mcp/README.md.

Use it

Ask it: Log today's work from my notes: … It looks up each animal, cage and experiment you mention, asks you when something could be more than one record, and sends one proposal with a link to it.

• The assistant reads what you can read, as you. Revoke its token under Settings → API tokens to cut it off.

What it can propose

• In the mouse colony, zebrafish, fly and worm databases and any other organism's: the everyday records. New animals, cages, tanks and vials; litters, weaning, moves and deaths; crosses, clutches and flips; weights and readings; scheduled jobs done.
• In an experiment: a step done, a readout, animals added, its status, a note.
• In the notebook: a line in the Log of today's daily log, with the time. If the page is open, the line appears in it within a few seconds.
• It can't delete anything, sign a page, or change who may see what.
• It can also tell you what is due, as Home lists it, and plan your day from it.

Approving

A proposal tells you (the bell) and waits under Proposed changes in your account menu.

• Each proposal is one summary in plain words: what will change in each database, with any warnings at the top (a litter date that would be replaced, pups too young to wean). Show each change lists every record, before → after.
• Approve makes every change at once; Discard makes none. There is no approving one change at a time: if something is wrong, discard it and ask the assistant for a corrected proposal.
• An approved proposal is one batch in Batch history, marked with the assistant's name, so Undo takes it back whole (a line added to the notebook stays).
• If a record it touches was changed after the proposal was made, or a change no longer goes through, nothing is applied and the page says which record and why.
• Only you can approve your proposals, and only signed in to BioManager: no token can. A proposal you leave waits two weeks, then expires.