Connect Codex, Claude, ChatGPT, or Cursor to Biohub MCP

Every client connects to the same server with the same settings:

Setting	Value
Server URL	`https://biohub.ai/mcp`
Transport	Streamable HTTP
Authentication	None. No sign-in or API key.
Suggested server name	`biohub`

After you connect, check the setup by asking your assistant to list the Biohub tools. You should see the seven tools listed in the Quickstart.

Codex

Codex CLI

Add the server

codex mcp add biohub --url https://biohub.ai/mcp

This writes the following to ~/.codex/config.toml, which you can also add by hand:

[mcp_servers.biohub]
url = "https://biohub.ai/mcp"

Check the connection

Run codex mcp list, or enter /mcp in a Codex session. The auth column reads Unsupported, which is expected because the server has no sign-in.

ChatGPT desktop app and Codex IDE extension

The ChatGPT desktop app, the Codex CLI, and the Codex IDE extension share one MCP configuration, which is separate from the developer-mode apps you add in ChatGPT on the web. If you already added biohub with the CLI, it’s available in the desktop app and the IDE extension too. To add it from the ChatGPT desktop app instead:

Open Settings, then select MCP servers.
Select Add server.
Enter biohub as the name, choose Streamable HTTP, and enter https://biohub.ai/mcp as the URL.
Save the server, then select Restart.

Type /mcp in the composer to see the connected servers. See the Codex MCP documentation for more options.

Claude Code

Add the server

claude mcp add --transport http biohub https://biohub.ai/mcp

Add --scope user to make it available in every project.

Check the connection

Run claude mcp list, or enter /mcp inside a session.

Use --transport http. An entry added with the sse transport can’t connect, as explained in Troubleshooting.

Claude.ai and Claude Desktop

Add Biohub MCP as a custom connector. Claude Desktop uses the connectors from your Claude account, so adding it once covers both.

Add the connector

Open Customize, then Connectors. Click +, then Add custom connector.

Enter the server

Enter https://biohub.ai/mcp as the remote MCP server URL and Biohub as the name if asked. Leave Advanced settings empty and click Add.

Turn it on in a chat

In a chat, click + at the lower left, choose Connectors, and turn on Biohub.

Check the connection

Ask the assistant to list the Biohub tools without calling them. You should see the seven tools listed in the Quickstart.

On Team and Enterprise plans, only an Owner can add a custom connector, under Organization settings, then Connectors. Members then find it under Customize, then Connectors, and click Connect. Free plans allow one custom connector.

ChatGPT

ChatGPT connects to custom MCP servers in developer mode. Developer mode is available on the web for Plus, Pro, Business, Enterprise, and Education accounts. On a workspace plan, an admin may need to allow it.

Turn on developer mode

In ChatGPT on the web, open Settings, then Security and login, and turn on Developer mode.

Create the app

Open chatgpt.com/plugins and select + to create a developer-mode app for a remote MCP server. Enter Biohub as the name and https://biohub.ai/mcp as the MCP server URL, choose No Authentication, and create it.

Use it in a chat

In a chat, choose Developer mode from the + menu and select Biohub.

Check the connection

Ask the assistant to list the Biohub tools without calling them. You should see the seven tools listed in the Quickstart.

ChatGPT displays the interactive Mol* structure viewer inline.

Cursor

Add the server

Add the server to ~/.cursor/mcp.json for all projects, or to .cursor/mcp.json in one project. Keep any servers already listed in the file.

{
  "mcpServers": {
    "biohub": {
      "url": "https://biohub.ai/mcp"
    }
  }
}

Check the connection

Check it in Cursor’s MCP settings, or run:

cursor-agent mcp list-tools biohub

Restart Cursor if it doesn’t pick up the change.

VS Code

VS Code uses MCP servers in Copilot Chat. If your organization manages GitHub Copilot, its policy must allow MCP servers.

Add the server

Run MCP: Add Server from the Command Palette and follow the prompts, or add this to .vscode/mcp.json in your workspace:

{
  "servers": {
    "biohub": {
      "type": "http",
      "url": "https://biohub.ai/mcp"
    }
  }
}

To add it for your user profile instead, run MCP: Open User Configuration and add the same entry.

Check the connection

Run MCP: List Servers to see its status. In Chat, select Configure Tools to see the Biohub tools and turn them on or off.

Other MCP clients

Any MCP client that supports Streamable HTTP can connect. Enter https://biohub.ai/mcp as the server URL and choose no authentication if the client asks. Don’t choose the older SSE transport. To check the server from a terminal, list its tools:

curl -s https://biohub.ai/mcp \
  -H 'Content-Type: application/json' \
  -H 'Accept: application/json, text/event-stream' \
  -H 'MCP-Protocol-Version: 2025-06-18' \
  -d '{"jsonrpc":"2.0","id":1,"method":"tools/list"}' | jq -r '.result.tools[].name'

The command prints the seven tool names. It uses jq to pick them out of the JSON-RPC response.

Next steps

Run a first request with the Quickstart.
Try the Example prompts.
If something doesn’t work, see Troubleshooting.

​Codex

​Codex CLI

​ChatGPT desktop app and Codex IDE extension

​Claude Code

​Claude.ai and Claude Desktop

​ChatGPT

​Cursor

​VS Code

​Other MCP clients

​Next steps

Codex

Codex CLI

ChatGPT desktop app and Codex IDE extension

Claude Code

Claude.ai and Claude Desktop

ChatGPT

Cursor

VS Code

Other MCP clients

Next steps