How to…

Connect an AI assistant

Step by step for each assistant app: add the BioManager plugin once, connect it to your lab, sign in, and try it.

Connecting takes a few minutes, once. Whatever app you use, it is the same four steps:

1. Check that your app can reach BioManager (the table below).
2. Add the BioManager plugin, where your app takes plugins. It teaches the assistant how to work with BioManager, so you never have to explain it.
3. Connect it to your lab with your BioManager's address, and sign in: BioManager opens in your browser and you press Allow. There is no password or token to give the assistant.
4. Try it: say I want to change something in BioManager.

Everything you need is on Help → Connect an AI assistant in BioManager (also under Settings → AI assistant & tokens), with your lab's address filled in, buttons for some apps and commands to copy for others. Keep it open beside this page.

Can your app reach BioManager?

An assistant app connects either from your own computer or from its company's servers on the internet. Which one decides what it can reach:

• On your computer: Claude Code, Codex, Cursor, VS Code, Cherry Studio, QwenWork (千问办公), Trae, Doubao (豆包) on the computer, Qwen Code, Kimi Code, and Claude Desktop with a token.
• In the cloud: claude.ai with the Claude desktop and phone apps' chats, and ChatGPT. They need the lab's server on the internet; its admin turns that on (the server's runbook, internet access). Until then, the Connect page says so and shows only the other ways.

The Connect page shows two addresses, both ending in /api/v1/mcp: the connector address (on the internet, for the cloud apps) and the address for apps on this computer or the lab network.

Claude

Claude on the web, the desktop app and the phone

Needs the lab's server on the internet. Do these on claude.ai or in the desktop app; the phone app then has it too.

1. Add the plugin. Open Customize → Plugins, choose Add → Add marketplace, enter gaspolymerase/biomanager, then open BioManager and press Add.Or download Plugin for Claude from the Download page and choose Add → Upload plugin with the zip. Once BioManager is listed in Claude's directory, you can find it under Discover instead.
2. Add the connector. Open the plugin's Connectors tab (or Customize → Connectors), choose Add custom connector, name it BioManager, and paste the connector address from the Connect page.
3. Connect. Press Connect. A BioManager page opens asking for a connection code. On the Connect page (on the lab network), press Get a connection code, type the code in, and press Allow. A code works once, for 10 minutes.
4. Try it. In a new chat, check BioManager is on in the chat's tools menu, and say I want to change something in BioManager. The first time, Claude asks before it uses each tool; choose Always allow for BioManager's tools. They can only read and propose: nothing changes until you approve it in BioManager.

Claude Code

Works with the desktop app and with a server on the lab network. In Claude Code:

1. Type /plugin marketplace add gaspolymerase/biomanager, then /plugin install biomanager@biomanager.
2. It asks for BioManager's MCP address: paste the address for this computer or the lab network from the Connect page.
3. Type /mcp, choose biomanager and Authenticate. BioManager opens in your browser: press Allow.
4. Say I want to change something in BioManager.

Without the plugin, the Connect page's one command connects it (claude mcp add …), or press Copy the message and send it to Claude Code: it sets itself up.

Claude Desktop, with a desktop app or a lab-network server

Claude Desktop's own connectors come from the internet, so for a BioManager it can't reach that way, it runs a small program from BioManager's source instead. On the Connect page, press Make a token: the next page shows the setup to paste into Claude Desktop (Settings → Developer → Edit Config), with your address and token in it. The steps, and the one command that installs what it needs, are in mcp/README.md. Claude Desktop's Code tab is Claude Code, and connects as above.

ChatGPT and Codex

ChatGPT

Needs the lab's server on the internet, and ChatGPT on the web: ChatGPT's phone apps don't take your own servers. ChatGPT lets a Business, Enterprise or Edu workspace make changes this way, once its admin turns on developer mode; on other plans it can only read.

1. Open Plugins, press + and choose Add custom MCP server.
2. Name it BioManager, paste the connector address, choose OAuth, and confirm with I understand and want to continue, then Create as a plugin and install it.
3. When it asks you to sign in, a BioManager page asks for a connection code: get one on the Connect page, type it in, and press Allow.
4. To have ChatGPT know BioManager without explaining it, add the plugin too: download Plugin for ChatGPT from the Download page, upload it at platform.openai.com/plugins and share it with your lab; each person then installs it. If someone in your lab already shared it with you, just install it.
5. In a chat, choose BioManager (type @) and say I want to change something in BioManager. Under its permissions, Allow read actions stops it asking before every look-up.

Codex

1. Add the plugin: codex plugin marketplace add gaspolymerase/biomanager, then install BioManager from its plugins.
2. Connect: codex mcp add biomanager --url <address> with the address for this computer or the lab network (the Connect page has the command with it filled in).
3. Sign in: codex mcp login biomanager. BioManager opens in your browser: press Allow.

Cursor and VS Code

1. On the Connect page, press Add to Cursor or Add to VS Code. The app opens and asks before adding BioManager: accept.
2. Sign in: the app shows that BioManager needs login, or asks you to allow it; BioManager opens in your browser, press Allow.
3. In VS Code, also add the plugin: run Chat: Install Plugin From Source with https://github.com/gaspolymerase/biomanager.

Assistants used in China

The DeepSeek, Qwen (千问) and Kimi chat apps can't connect to other apps yet. These can, from a computer that reaches BioManager.

Cherry Studio, with DeepSeek, Qwen, Kimi or GLM

1. Set up Cherry Studio with your model's key (DeepSeek, Qwen, Kimi or Zhipu GLM), as Cherry Studio describes.
2. On the Connect page, press Add to Cherry Studio. Cherry Studio opens with BioManager added, switched off: switch it on in Settings → MCP.
3. Sign in when BioManager opens in your browser: press Allow.
4. In a chat, turn on the BioManager tools and say I want to change something in BioManager.

QwenWork (千问办公), Trae and Doubao (豆包)

These take your BioManager's address with a token. On the Connect page, press Make a token; the next page shows the setup, with the address and token filled in.

• QwenWork: 扩展 → 连接器 → + 添加 → 粘贴 JSON 配置, and paste the JSON.
• Trae: 设置 → MCP → 添加 → 手动添加, and paste the same JSON.
• Doubao on the computer: 技能 · 连接器 → 新建 → 新建自定义连接器, transport HTTP, the address, and a header Authorization with the value Bearer and the token.

The token is shown once: keep it in the app, not in a note. Revoke it under Settings → AI assistant & tokens when you stop using the app.

Qwen Code and Kimi Code

• Qwen Code: add the plugin with qwen extensions install https://github.com/gaspolymerase/biomanager:biomanager, then connect with qwen mcp add --transport http biomanager <address>. It signs in by itself in your browser.
• Kimi Code: kimi mcp add -t http biomanager <address> --auth oauth, then kimi mcp auth biomanager.

Claude Code on DeepSeek or GLM

DeepSeek and Zhipu (GLM) both offer an address that speaks Claude's API, so Claude Code, with the BioManager plugin, can run on a DeepSeek or Zhipu key. Set Claude Code up as their own pages say (DeepSeek's Anthropic API guide, Zhipu's Claude Code guide), then follow Claude Code above.

Any other app

An app that takes an MCP server (Goose, OpenCode, LobeHub, Chatbox and others) needs the address, as a streamable HTTP server. If it signs in with OAuth, leave the headers empty and sign in in the browser; if it doesn't, press Make a token and give it the header the next page shows. An app that only starts commands runs mcp/biomanager_mcp.py, as for Claude Desktop.

Check that it works

1. Say I want to change something in BioManager. It should show you what's due today and ask what you did, without asking you how BioManager works.
2. Tell it one small real thing, e.g. weighed mouse 1043, 24.1 g. It looks the mouse up, sends one proposal, and gives you a link.
3. Open the link (or the bell) in BioManager: the proposal waits under Proposed changes. Read it, and press Approve or Discard.

The connection is listed under Settings → AI assistant & tokens with the app's name. Revoke it there to end it; the assistant then can't read anything.

Related: AI assistants Scripts and the API Run it for your lab