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How to connect Synthesize Bio MCP to Claude

Connect Claude Web, Desktop and 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

Claude is Anthropic's AI assistant, available on the web, in the desktop app, and on mobile. Cowork is its agent for knowledge work, and it runs on all of those surfaces too. Connected to your apps, Claude can work with your files and services to accomplish complex tasks on your behalf.

This guide walks you through the easiest and most secure way to connect your Synthesize Bio account to Claude 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.

Setup is the same on Claude Web, Desktop, and Cowork, and you only need to do it once. The connector is tied to your account, so it's available in all three.

Also integrate Synthesize Bio MCP with

ChatGPTHermesAtomic Agent

Connecting Synthesize Bio to Claude Web, Desktop, and Cowork

Two ways to add the Composio connector. Pick whichever you prefer.

1. Add with one click

Click the button. Claude opens with the Composio connector filled in. Click Add, then go to step 2.

Add to Claude

Add manually

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

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

2. 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 Web, Desktop, and Cowork

3. Connect your Synthesize Bio account

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

For example, ask Claude 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 Claude, and your Synthesize Bio account is ready to use.

What is the Synthesize Bio Claude Connector, 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.

Troubleshooting

1. Why does Claude not use the Composio connector for Synthesize Bio?

The connector can show as connected, but Claude must use it in each Synthesize Bio conversation.

  • Click + at the lower left of the chat, or type /.
  • Hover Connectors.
  • Turn on Composio.
  • Ask Claude to connect to Synthesize Bio again.

2. Why does Claude show an MCP server error before Synthesize Bio connects?

Claude can show Couldn't reach the MCP server or Authorization with the MCP server failed when you add the connector for Synthesize Bio.

  • Check that the connector URL is https://connect.composio.dev/mcp.
  • Connectors run from Anthropic's cloud, so your device network is usually not the problem.
  • Add the connector again from Customize > Connectors, then ask Claude to connect Synthesize Bio.
  • If it fails again, send the error and the ofid_ reference id to support@composio.dev.

3. Why does the Synthesize Bio authorization link not work?

The Composio connector is one server. Your Synthesize Bio account connects separately when Claude asks for it.

  • If the browser does not open, or the link expires, ask Claude to retry the Synthesize Bio connection.
  • Composio creates a fresh Synthesize Bio authorization link.
  • Open that link in your browser and finish the Synthesize Bio sign-in.

4. Why do Synthesize Bio actions fail after they worked before?

The Synthesize Bio connection can expire or lose permission.

  • Ask Claude to inspect the Synthesize Bio connection.
  • If the connection is unhealthy, disconnect it when Claude prompts you.
  • Reconnect the Synthesize Bio account and retry the action.
  • If Claude shows a permission prompt, approve it before Claude changes data in Synthesize Bio.
  • If the action still fails with a permission error, check that the connected account has that permission in Synthesize Bio itself.

5. How do I switch to a different Synthesize Bio account?

Claude can manage the Synthesize Bio connection for you.

  • Ask Claude to disconnect or delete the current Synthesize Bio account.
  • Ask Claude to connect Synthesize Bio again.
  • Open the new Composio authorization link for Synthesize Bio.
  • Sign in with the other Synthesize Bio account in the browser.
  • After the account connects, ask Claude to retry the Synthesize Bio task.

6. Why is my Synthesize Bio connection missing in Claude Desktop or on a Team plan?

The connector belongs to your Claude account, so your Synthesize Bio connection works in Claude Web, Desktop, and Cowork.

  • In Claude Desktop, open Customize > Connectors.
  • Next to Composio, click ⋮ and click Clear cache.
  • If Synthesize Bio tools still do not appear, click ⋮, disconnect, remove the connector, and add it again.
  • On Team or Enterprise, an Owner or Primary Owner must enable the connector before you can connect Synthesize Bio.
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

ChatGPT logo

ChatGPT

Use Synthesize Bio MCP with ChatGPT

Hermes logo

Hermes

Use Synthesize Bio MCP with Hermes

Atomic Agent logo

Atomic Agent

Use Synthesize Bio MCP with Atomic Agent

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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