How to integrate Synthesize Bio MCP with Hermes

Connect Hermes 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

Hermes is a 24/7 autonomous agent that lives on your computer or server — it remembers what it learns and evolves as your usage grows.

This guide explains the easiest and most robust way to connect your Synthesize Bio account to Hermes. You can do this through either Composio Connect CLI or Composio Connect MCP. For personal use we recommend the CLI, but you won't go wrong with MCP either.

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What is Composio Connect?

Composio Connect is a consumer offering that lets anyone plug 1,500+ applications directly into their agent harness — including Hermes. It can:

  • Search and load tools from relevant toolkits on-demand, reducing context usage.
  • Chain multiple tools to accomplish complex workflows via a remote workbench, without excessive back-and-forth with the LLM.
  • Manage app authentication end-to-end with zero manual overhead.

Integrating Synthesize Bio with Hermes

Using Composio Connect CLI

1. Install the Composio CLI

Run the install script directly, or paste https://composio.dev/hermes into your Hermes chat box to have it installed for you.

bash
curl -fsSL https://composio.dev/install | bash
Hermes authenticating with Composio

2. Authenticate

Once the CLI is installed, ask Hermes to authenticate with Composio.

3. Connect to Synthesize Bio

Ask your agent to connect to Synthesize Bio, or simply request any Synthesize Bio-related task. Hermes will prompt you to authenticate and authorize access.

4. Done. You're all set with a new Synthesize Bio connection.


Using Composio Connect MCP

1. Get your MCP URL and API Key

Go to dashboard.composio.dev and copy your Connect MCP URL and API key.

Copy MCP URL and API key from Composio dashboard

2. Open the Hermes config file

bash
nano ~/.hermes/config.yaml

3. Add the Composio Connect MCP server

bash
mcp_servers:
  composio:
    url: "https://connect.composio.dev/mcp"
    headers:
      x-consumer-api-key: "YOUR_COMPOSIO_API_KEY"
    connect_timeout: 60
    timeout: 180

Save with Ctrl + O, Enter, then exit with Ctrl + X.

4. Restart your Hermes agent

Once restarted, ask your agent to connect to Synthesize Bio or request any Synthesize Bio-related task. It will prompt you to authenticate and authorize access.

5. Done!

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.

Way Forward

With Synthesize Bio connected, Hermes can now act on your behalf whenever it detects a relevant task or you ask it to.

From here, you can extend Hermes further:

  • Connect more apps: Calendar, Slack, Notion, Linear, and hundreds of others are available through the same Composio Connect setup. Each new integration compounds what Hermes can do for you.
  • Build workflows across tools: Once multiple apps are connected, Hermes can chain actions together — turn an email into a calendar invite, a Slack message into a Linear ticket, or a meeting note into a follow-up draft.
  • Let it learn your patterns: The more you use Hermes, the better it gets at anticipating how you'd handle recurring tasks. Give it feedback on drafts and decisions, and it will adapt.

If you run into trouble or want to share what you've built, join the community or check out the Docs for deeper configuration options.

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.

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. Hermes 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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