Sign in to GeneBe MCP

The public GeneBe MCP URL needs no account. If you would rather have your assistant work under your own GeneBe account, connect it to the signed-in URL instead:

https://mcp.genebe.net/v1/account/mcp

You sign in on genebe.net, in your browser, and decide what the assistant may do. The assistant never sees your password.

What you get

Today the signed-in URL offers the same tools as the public one, plus:

Tool	What it does
get_my_account	Shows which GeneBe account the assistant is signed in as, your plan and today's usage.
search_my_samples	Lists and searches your samples (your own and those shared with your organizations), newest first. Filter by words, project, sequencing id, experiment type (WGS, TRIO, ...), status, labels, organization and creation date.
get_my_sample	Shows one sample: status, labels, tags, trio or pair members, input file names and quality metrics.

Your requests are counted against your account's daily limits instead of the shared limit for anonymous users. The sample tools only read, and only with the permission you give on the consent screen (see what you are agreeing to). More tools for your own data are planned (see the roadmap).

Try asking: "What samples do I have?", "Show my trios created in the last 30 days that are ready to view", "Which samples in project cardio have the label urgent?"

Connect

Claude Code

claude mcp add --transport http genebe https://mcp.genebe.net/v1/account/mcp

Then:

1. In Claude Code run /mcp, choose genebe and select Authenticate.
2. Your browser opens on genebe.net. Sign in if you are asked to.
3. Check the screen: it names the application asking for access and lists what it will be able to do. Click Allow.
4. Go back to Claude Code. To confirm, ask "Which GeneBe account am I signed in as?"; the assistant calls get_my_account.

Already added the public URL?

Server names are unique. If you added the public URL as genebe earlier, either remove it first with claude mcp remove genebe, or give the signed-in one another name, for example claude mcp add --transport http genebe-account https://mcp.genebe.net/v1/account/mcp.

Other assistants

Any client that supports MCP authorization (OAuth) starts the sign-in by itself when you add the signed-in URL, usually by opening your browser. Use the URL above in place of the public one:

• Claude (web and desktop): Settings → Connectors → Add custom connector.

• ChatGPT: chatgpt.com/plugins → Add (+) → Add custom MCP.

• Cursor (~/.cursor/mcp.json):

  { "mcpServers": { "genebe": { "url": "https://mcp.genebe.net/v1/account/mcp" } } }

• VS Code (.vscode/mcp.json):

  { "servers": { "genebe": { "type": "http", "url": "https://mcp.genebe.net/v1/account/mcp" } } }

What you are agreeing to

The consent screen shows the permissions the assistant asks for, and you can untick any of them. There are two:

• Look up and classify variants and genes using GeneBe public data. No access to your data.
• See the list of your samples and their basic details (read only). The assistant can list and search your samples and read their basic details. It cannot change, delete or upload anything, and it never receives clinical data: phenotype, diagnosis, sex, dates of birth and collection, origin and storage paths are left out. Sample names and sequencing ids are sent, so keep in mind that they can identify a person.

If you untick the second one, the sample tools answer that access was not granted. If you untick everything, Allow is disabled. Connected before samples were available? Disconnect in Connected Apps and connect again to approve the new permission.

You stay connected while you use the assistant. Access renews itself in the background, and if you do not use it for about 30 days you are asked to sign in again.

Disconnect

Open Settings → Connected Apps on genebe.net. Every assistant and device connected to your account is listed with its permissions and when it was last used. Disconnect removes its access immediately; the assistant can no longer act as you, and to use it again you sign in anew.

Privacy

• GeneBe remembers which assistants you connected (name, permissions, last use) so that you can manage them. Access tokens are stored only as hashes.
• The MCP server stores nothing about your questions, and variant input is not logged.
• What an assistant reads becomes part of your conversation with the AI service you use it with. Keep that in mind when you ask about your own samples.
• GeneBe MCP is for research use only; see the overview.

Troubleshooting

• "401" or "authentication required" before signing in is expected: it is how the assistant learns it has to start the sign-in. Authenticate as described above.
• The browser did not open (for example over SSH): copy the address your assistant prints into a browser on any machine, finish there, and the assistant continues.
• "This request is invalid or has expired" on the consent screen: start the connection again from the assistant. A request is valid for 15 minutes.
• It stopped working after a while: you may have disconnected it in Connected Apps, or not used it for about 30 days. Authenticate again.