SIGN UPLOG IN
X (Twitter)LinkedInGitHubDiscordYouTube

How to connect Synthesize Bio MCP with ChatGPT

Connect ChatGPT 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.

Get started for freeGet a demo
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

How to connect Synthesize Bio MCP with ChatGPT

ChatGPT can take action across your apps and files, stay with a project for hours, and turn a goal into finished materials like sheets, slides, and docs, not just answers.

In this guide, I will explain the easiest and most secure way to connect your Synthesize Bio account to ChatGPT via Composio Connect, so it can run bulk analyses, launch single-cell pipelines, monitor job status, fetch results, and manage your configs through natural language commands without ever putting your account credentials at risk.

Also integrate Synthesize Bio MCP with

Claude CoworkHermesAtomic Agent

Why use Composio over default connectors?

  • Apps with read and write access. Default connectors mostly can read your data. Composio's Synthesize Bio integration lets ChatGPT take actions like creating drafts, sending updates, labeling records, and more.
  • 1,500+ SaaS toolkits out of the box. Composio gives you instant access to a vast catalog of pre-built connectors, from Gmail and Slack to Notion, Linear, and Salesforce.
  • One MCP server for every app. Connect any of your applications on demand through a single endpoint, rather than juggling a separate server for each app.
  • Smart, context-aware tool loading. Unlike traditional MCP servers that dump every available tool into the LLM context window, Composio searches for and loads only the tools relevant to the task at hand.
  • Cross-app automation. Chain actions across multiple apps in a single run - fetch a thread, summarize it in Notion, and post highlights to Slack without leaving the conversation.

Prerequisites

  • A ChatGPT account. We will use the ChatGPT desktop app, and the steps are the same on the web.
  • Access to the Synthesize Bio workspace you want to connect.
  • Composio plugin.

Note: Composio connects through OAuth. You will be asked to sign in and approve specific permissions. Review the permission screen carefully if you are using a work account.

Step-by-step: Connect Synthesize Bio to ChatGPT

1. Install the Composio plugin

Click the button. ChatGPT opens the Composio plugin page. Click Install plugin.

Install in ChatGPT

Composio plugin page in ChatGPT with the Install plugin button

You can also find it inside ChatGPT: go to Settings, open Plugins, search the marketplace for Composio, and click Install plugin.

2. Authenticate

After you install, ChatGPT asks you to authenticate with Composio. Log in and click Allow access to authorize ChatGPT to use your Composio account.

Composio login and Allow access screen for ChatGPT

3. Start using Composio

That is it. Composio tools are now available in ChatGPT. Type @Composio followed by your request, for example @Composio find unread Synthesize Bio messages and summarize them, and it will run the actions you authorize. On first use it asks you to authorize Synthesize Bio.

Option 2: Add Composio as an MCP server

If you cannot use the plugin marketplace, add Composio as a custom MCP server instead.

1. Open the MCP settings

In ChatGPT, go to Settings and open the Plugins section. Inside the Plugins page, click the MCP tab.

ChatGPT settings showing the Plugins page with the MCP tab selected

2. Add the server

Click Add server. In the Name field enter Composio, for Type select Streamable HTTP, and in the URL field paste the Composio MCP server URL:

bash
https://connect.composio.dev/mcp
ChatGPT Add server dialog with the name Composio, type Streamable HTTP, and the Composio MCP URL

Then click Save. The Composio server now appears in your MCP plugins list.

ChatGPT Plugins page showing the Composio MCP server added to the list

3. Authenticate

Click Authenticate on the Composio entry, log in via Composio, and click Allow access. Composio tools are then available in ChatGPT the same way as with the plugin.

What you can do after connecting Synthesize Bio

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

Security + privacy notes (important)

  • Use least-privilege access: Only grant permissions you actually need.
  • Review OAuth permissions before approving: Make sure requested scopes match what you expect Composio and ChatGPT to do.
  • Keep write actions human-reviewed: For actions like sending messages, creating labels, or editing drafts, keep manual confirmation enabled.
  • Be careful with sensitive data: Avoid using this setup with highly sensitive information unless allowed by your personal, company, or client policies.
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

Claude Cowork logo

Claude Cowork

Use Synthesize Bio MCP with Claude Cowork

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. ChatGPT 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.

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.

Start building