Synthesize Bio MCP for AI Agents

Securely connect your AI agents and chatbots (Claude, ChatGPT, Cursor, etc) with Synthesize Bio MCP or direct API to start analyses, monitor job status, fetch results, and manage experiment configurations through natural language.

Synthesize Bio MCP logoSynthesize Bio MCP
Dcr Oauth

Synthesize Bio MCP is a toolkit that runs bulk and single-cell gene-expression analyses from natural-language experiment requests. Use it to translate experiment intents into reproducible pipelines and monitor results without bespoke integration.

5 Tools

Try Synthesize Bio MCP now

Type what you want done — sign in and watch it run live in the Tool Router playground.

TOOL ROUTER PLAYGROUND
Synthesize Bio MCP
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TOOLS

Supported Tools

Every Synthesize Bio MCP action and event your agent gets out of the box.

Analyze gene expression

Starts a differential gene expression analysis using Synthesize Bio's AI platform.

Get analysis results

Polls the status of a gene expression analysis.

Get counts data url

Returns a presigned S3 URL to download the raw gene expression counts data (JSON) produced by a completed or in-progress analysis job.

Get metadata schema

Returns the structured-metadata schema used to turn a natural-language experiment description into sample groups.

Resolve sample metadata

Deterministically harmonizes already-structured sample `groups` to Synthesize Bio's controlled ontology vocabulary.

SETUP GUIDE

Connect Synthesize Bio MCP Tool with your Agent

1

Install Composio

typescript
npm install @composio/core ai @ai-sdk/openai @ai-sdk/mcp
Install the Composio SDK for Python or TypeScript
2

Initialize Client and Create Tool Router Session

typescript
import { Composio } from '@composio/core';

const composio = new Composio({ apiKey: 'your-api-key' });
const session = await composio.create('your-user-id');
console.log(`Tool Router session created: ${session.mcp.url}`);
Import and initialize the Composio client, then create a Tool Router session for Synthesize Bio MCP
3

Connect to AI Agent

typescript
import { openai } from '@ai-sdk/openai';
import { experimental_createMCPClient as createMCPClient } from '@ai-sdk/mcp';
import { generateText } from 'ai';

const client = await createMCPClient({
  transport: {
    type: 'http',
    url: session.mcp.url,
    headers: {
      'x-api-key': 'your-composio-api-key',
    },
  },
});

const tools = await client.tools();
const { text } = await generateText({
  model: openai('gpt-4o'),
  tools,
  messages: [{
    role: 'user',
    content: 'YOUR_SPECIFIC_PROMPT_HERE'
  }],
  maxSteps: 5,
});

console.log(`Agent: ${text}`);
Use the MCP server with your AI agent (Anthropic Claude or Mastra)
SETUP GUIDE

Connect Synthesize Bio MCP API Tool with your Agent

1

Install Composio

typescript
npm install @composio/openai
Install the Composio SDK
2

Initialize Composio and Create Tool Router Session

typescript
import OpenAI from 'openai';
import { Composio } from '@composio/core';
import { OpenAIResponsesProvider } from '@composio/openai';

const composio = new Composio({
  provider: new OpenAIResponsesProvider(),
});
const openai = new OpenAI({});
const session = await composio.create('your-user-id');
Import and initialize Composio client, then create a Tool Router session
3

Execute Synthesize Bio MCP Tools via Tool Router with Your Agent

typescript
const tools = session.tools;
const response = await openai.responses.create({
  model: 'gpt-4.1',
  tools: tools,
  input: [{
    role: 'user',
    content: 'YOUR_SPECIFIC_PROMPT_HERE'
  }],
});
const result = await composio.provider.handleToolCalls(
  'your-user-id',
  response.output
);
console.log(result);
Get tools from Tool Router session and execute Synthesize Bio MCP actions with your Agent

Why Use Composio?

AI Native Synthesize Bio MCP Integration

  • Supports both Synthesize Bio MCP and direct API based integrations
  • Structured, LLM-friendly schemas for reliable tool execution
  • Rich coverage for reading, writing, and querying your Synthesize Bio MCP data

Managed Auth

  • Built-in OAuth handling with automatic token refresh and rotation
  • Central place to manage, scope, and revoke Synthesize Bio MCP access
  • Per user and per environment credentials instead of hard-coded keys

Agent Optimized Design

  • Tools are tuned using real error and success rates to improve reliability over time
  • Comprehensive execution logs so you always know what ran, when, and on whose behalf

Enterprise Grade Security

  • Fine-grained RBAC so you control which agents and users can access Synthesize Bio MCP
  • Scoped, least privilege access to Synthesize Bio MCP resources
  • Full audit trail of agent actions to support review and compliance
FRAMEWORKS

Use Synthesize Bio MCP with any AI Agent Framework

Choose a Framework you want to connect Synthesize Bio MCP with

FAQ

Frequently asked questions

Yes, Synthesize Bio MCP requires you to configure your own Dcr Oauth credentials. Once set up, Composio handles secure credential storage and management for you.

Yes! Composio's Tool Router enables agents to use multiple toolkits. Learn more.

Composio is SOC 2 and ISO 27001 compliant with all data encrypted in transit and at rest. Learn more.

Composio maintains and updates all toolkit integrations automatically, so your agents always work with the latest API versions.

Start with Synthesize Bio MCP.It takes 30 seconds.

Managed auth, hosted MCP servers, and every Synthesize Bio MCP tool your agent needs.Free to start.

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