Get Started

How it works

1. 1

   Find a tool

   Browse or search the registry for the bioinformatics tool you need. Each listing shows a description, keywords, README, and install instructions. For Hi-C analysis, search "hic" or "hi-c".

2. 2

   Copy the MCP config

   On the tool's page, copy the ready-made MCP server config block. This tells your AI assistant (Claude Desktop, Cursor, etc.) how to launch the tool.

3. 3

   Add it to your client

   Open your AI client's settings file (e.g. claude_desktop_config.json) and paste the config under "mcpServers". Save and restart the client.

4. 4

   Start using it

   The tool is now available as a callable function inside your AI assistant. Ask it to run Hi-C analysis — it will invoke the MCP server on your behalf.

Example — Hi-C analysis

Hi-C is a chromosome conformation capture technique used to map 3-D genome organisation genome-wide. The hic-mcp tool exposes Hi-C processing pipelines (contact matrix generation, compartment calling, TAD detection, and more) as MCP functions your AI assistant can call directly.

1. Search the registry

Go to Search and type hic. Open the hic-mcp package page to read its README and available functions.

2. Add to your client config

Paste the snippet below into your AI client's MCP config file:

{
  "mcpServers": {
    "hic-mcp": {
      "command": "npx",
      "args": ["-y", "hic-mcp"],
      "env": {}
    }
  }
}

3. Ask your AI to run it

Restart the client, then prompt your assistant:

Use hic-mcp to generate a contact matrix from my .fastq files
and identify topologically associating domains (TADs).

The assistant will call the correct MCP functions, pass your files, and return the processed results — no manual CLI required.

Supported AI clients

Any client that supports the Model Context Protocol works with AIBioAgentTools tools:

Have a tool to share?

If you've built a bioinformatics MCP server, publish it to the registry so the community can discover and use it. All it takes is a GitHub repo with a README.