How to connect Synthesize Bio MCP to Claude Cowork

Connect Claude Cowork to Synthesize Bio MCP. Run differential expression on latest samples, start single-cell pipeline for patient sample, and more using natural language, with authentication handled for you.

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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

Introduction

Cowork is Anthropic's AI agent for knowledge work. Think of it as Claude Code for everything else. It works autonomously with your computer, local files, and applications to accomplish complex tasks.

This guide walks you through the easiest and most secure way to connect your Synthesize Bio account to Cowork via Composio Connect, enabling it to run differential expression on latest samples, start single-cell pipeline for patient sample, fetch results and generate QC summary report, and more such actions on your behalf without compromising your account security.

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Connecting Synthesize Bio to Claude Cowork

1. Open Customize

In Claude Desktop, click Customize in the left sidebar, then select Connectors and click the + icon at the top.

Claude Desktop connectors screen with Add custom connector selected

2. Add the Composio MCP server

Click Add custom connector and paste in the Composio MCP server URL:

bash
https://connect.composio.dev/mcp
Add custom connector dialog with Composio MCP server URL

3. Authorize in your browser

Click Connect. You'll be redirected to a browser window where you can authorize Composio to continue.

Composio authorization screen for Claude Cowork

4. Connect your Synthesize Bio account

Back in Cowork, ask the agent to connect to Synthesize Bio or give it any Synthesize Bio-related task.

For example, ask Cowork to:

  • "Run differential expression on latest samples"
  • "Start single-cell pipeline for patient sample"
  • "Fetch results and generate QC summary report"

It will prompt you to authenticate and authorize access.

That's it. Composio's tools are now available in Cowork, and your Synthesize Bio account is ready to use.

What is Claude Cowork?

Claude Cowork is Anthropic's agent for general knowledge work. It can use your computer, files, and connected applications to complete longer-running tasks across your work tools.

With Composio Connect, Cowork can securely access apps like Synthesize Bio through MCP without you sharing account credentials directly with the agent.

What is the Synthesize Bio MCP server, and what's possible with it?

The Synthesize Bio MCP server is an implementation of the Model Context Protocol that connects your AI agent and assistants like Claude, Cursor, etc directly to your Synthesize Bio account. It provides structured and secure access so your agent can perform Synthesize Bio operations on your behalf.

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.

FRAMEWORKS

How to build Synthesize Bio MCP Agent with another framework

FAQ

Frequently asked questions

With a standalone Synthesize Bio MCP server, the agents and LLMs can only access a fixed set of Synthesize Bio tools tied to that server. However, with the Composio Tool Router, agents can dynamically load tools from Synthesize Bio and many other apps based on the task at hand, all through a single MCP endpoint.

Yes, you can. Claude Cowork fully supports MCP integration. You get structured tool calling, message history handling, and model orchestration while Tool Router takes care of discovering and serving the right Synthesize Bio tools.

Yes, absolutely. You can configure which Synthesize Bio scopes and actions are allowed when connecting your account to Composio. You can also bring your own OAuth credentials or API configuration so you keep full control over what the agent can do.

All sensitive data such as tokens, keys, and configuration is fully encrypted at rest and in transit. Composio is SOC 2 Type 2 compliant and follows strict security practices so your Synthesize Bio data and credentials are handled as safely as possible.

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