Biomni MCP connector for AI agents

Biomni MCP tools for AI agents

CALL ANY TOOL

10 tools covering create, list.

biomnimcp_create_project

Create a new biomni project in the caller's current workspac

Create a new biomni project in the caller's current workspace. a project is a persistent container with its own file drive where tasks and uploaded files live. only create a project when the user explicitly asks for a new one; call list_projects first to check if a suitable one already exists.

Parameters

Name

Type

Required

Description

name

string

Required

Human-readable project name. Required.

description

string

Optional

Optional free-text description of the project.

metadata

string

Optional

Optional arbitrary key-value pairs stored alongside the project for your own use (e.g. external system IDs).

biomnimcp_list_projects

List the caller's projects in the active workspace. always c

biomnimcp_list_result_files

List the names and metadata of output files produced by an a

biomnimcp_list_tasks

List tasks in a project. returns the tasks belonging to the

biomnimcp_list_workspaces

List the workspaces (orgs) the caller belongs to and show wh

biomnimcp_send_message

Send a user message to an existing biomni task and trigger a

biomnimcp_start_new_task

Auto-create a biomni task in a project and send the first me

biomnimcp_switch_workspace

Switch the caller's active workspace so that subsequent call

biomnimcp_upload_file

Upload a small text file (vcf, csv, tsv, json, or code) to a

biomnimcp_wait_for_next_update

Long-poll for the next batch of progress on the agent's curr

Build your Agent

Same auth pattern across every framework.

from langchain_mcp_adapters.client import MultiServerMCPClient
from scalekit import ScalekitClient

client = ScalekitClient(env_url=ENV_URL, client_id=CLIENT_ID, client_secret=SECRET)
token = client.agent.get_token(user_id="user_id", connector="biomnimcp")

mcp = MultiServerMCPClient({
    "biomnimcp": {
        "url": "https://mcp.scalekit.com/biomnimcp",
        "headers": {"Authorization": "Bearer " + token}
    }
})
tools = await mcp.get_tools()

import OpenAI from "openai";
import { ScalekitClient } from "@scalekit-sdk/node";

const client = new ScalekitClient({ envUrl, clientId, clientSecret });
const token = await client.agent.getToken({ userId: "user_id", connector: "biomnimcp" });

const openai = new OpenAI();
// Connect to MCP at https://mcp.scalekit.com/biomnimcp
// Pass: Authorization: Bearer + token

import Anthropic from "@anthropic-ai/sdk";
import { ScalekitClient } from "@scalekit-sdk/node";

const client = new ScalekitClient({ envUrl, clientId, clientSecret });
const token = await client.agent.getToken({ userId: "user_id", connector: "biomnimcp" });

const anthropic = new Anthropic();
// Connect to MCP at https://mcp.scalekit.com/biomnimcp
// Pass: Authorization: Bearer + token

from google.adk.agents import LlmAgent
from scalekit import ScalekitClient

client = ScalekitClient(env_url=ENV_URL, client_id=CLIENT_ID, client_secret=SECRET)
token = client.agent.get_token(user_id="user_id", connector="biomnimcp")
# Connect to MCP at https://mcp.scalekit.com/biomnimcp
# Pass: Authorization: Bearer + token

Try these prompts

Paste any prompt into your agent to get started.

Get started

Copy the prompt

Copied

Create a new Biomni project in the caller’s current workspace?

Copy the prompt

Copied

List the caller’s projects in the active workspace?

Advanced

Copy the prompt

Copied

Send a user message to an existing Biomni task and trigger AI agent execution?

Copy the prompt

Copied

Auto-create a Biomni task in a project and send the first message in a single call, triggering AI agent execution?

SEE HOW AUTH WORKS

User authorises once. Every agent call after uses their token with scope enforcement.

Authorize

Your user connects

Biomni MCP

once. We tie it to their identity and the meetings they approved — no shared bot account, no org-wide access

Who:

user ‘A’

when:

Once per user

access:

Limited to user

Store

Their

Biomni MCP

token lives in a vault scoped to them. User A's meetings are never reachable by an agent acting for user B, even on the same connection

vault:

encrypted

scope:

per-user

tokens:

auto-refreshed

Resolve

When your agent calls a

Biomni MCP

tool, we fetch the right token server-side. It never touches your agent, never appears in the LLM context, never shows up in your logs

speed:

~40ms

check:

before every call

seen by:

nobody

Audit

Every

Biomni MCP

tool call is logged — who triggered it, which meeting was fetched, what came back. 90 days of history, tied to the user who authorized it

history:

90 days

export:

SIEM-ready

logged:

every call

Test other agents

See the same per-user auth pattern across other connectors.

SALES

Deal intelligence agent

Combine Gong, Attio, and Slack signals to surface deal risks and next-best actions. Updated after every call.

ENGINEERING

Engineering standup agent

Aggregate GitHub and GitLab activity, link to Jira, and post a daily standup digest to Slack. No async updates.

Why Scalekit

Secure your agent's access. Connectors ship in minutes

Other connector libraries treat auth as a demo afterthought.

01.

Shared tokens break per-user analytics

A shared token looks fine in a demo. In production every call looks like a service account. Scalekit resolves the real user credential.

// shared token
 audit → bot_service_account

 // scalekit
 audit → user_abc ✓

02.

Authentication is not authorization

03.

Multi-tenancy is architectural

04.

One connector today. Ten tomorrow.

“Our agents act across Salesforce, Gong, Google Drive, and more, on behalf of every customer. Scalekit behind the scenes meant we can keep adding tools without ever rebuilding how credentials or tool calling work.”

Venu Madhav Kattagoni

Head of Engineering / Von

FAQs

Frequently Asked Questions

Does the agent access Biomni as the user or as a shared key?
As the user. Each workspace member authorizes once and Scalekit resolves their credential at request time. Audit logs attribute every action to that user, not a shared service account.

Where is the Biomni OAuth token stored?
In Scalekit's managed AES-256 token vault, namespaced per tenant. Refresh is automatic. Revocation is a single dashboard action. Tokens never appear in prompts, logs, or LLM context.

Can I limit what the agent is allowed to do in Biomni?
Yes. Pass a tool name filter to listScopedTools so the analytics agent only sees the subset you authorize. Pre-API-call scope checks block out-of-policy actions before the request reaches Biomni.

What happens when a user revokes Biomni access?
The connection is invalidated on the next tool call. Subsequent requests for that user fail closed with a clear error. Other users in the tenant remain unaffected. The event is logged for audit.

Are biomedical analyses isolated per researcher?
Yes. Projects, tasks, and result files stay inside the authorizing user's Biomni workspace. Genomic data and analysis outputs never cross user boundaries.

On this page

Tool and actions Framework Compatibility Starter Prompt Auth Lifecycle Try Other Agents Why Scalekit