OmicsBox Engine · AI Agents

Run OmicsBox analyses by asking your AI assistant

Connect OmicsBox to Claude, Claude Science, ChatGPT or your coding assistant. Ask in everyday language, and the assistant finds the right OmicsBox tool, runs it on your data in OmicsCloud and gives you a link to the results. No code, no command-line options, nothing to install.

Connect your assistant Join Early Access

What is an MCP?

A standard plug between AI assistants and real tools

The Model Context Protocol (MCP) is an open standard that lets AI assistants use external tools. OmicsBox provides an MCP server, so any compatible assistant can browse the OmicsBox tool catalogue and run analyses on your behalf. The assistant does not run the analyses itself: OmicsCloud does, exactly as when you start a cloud tool from OmicsBox Desktop.

1

You ask

Describe the analysis in your own words.

2

The assistant picks the tool

It looks up the matching OmicsBox tool, reads its parameters and asks you about anything unclear.

3

OmicsCloud runs it

The job runs in the background on your OmicsBox account. Come back later and ask how it is going.

4

You open the results

Results are saved to your cloud storage, with a link that opens them in OmicsBox Web.

Claude Science and more

Bioinformatics inside the assistant you already use

In Claude Science, add OmicsBox as a remote connector and run OmicsBox tools right from your research conversations. The same connection works in the other assistants that support custom connectors.

  • Claude (web and desktop) and Claude Science
  • ChatGPT (developer mode)
  • Claude Code and Codex
  • Cursor, VS Code and Windsurf

What you can ask

  • “Which OmicsBox tools can I use to annotate a set of protein sequences?”
  • “Run InterProScan on proteins.fasta in my Uploads folder.”
  • “Run a differential expression analysis with DESeq2 on counts.txt, comparing treated and control samples.”
  • “How is my job going?”
  • “Show me the results of my last run.”

Setup is easy

Connected in about a minute

Every assistant uses the same server address. You do not need to copy a key or a password: the assistant opens an OmicsBox sign-in page and you approve the connection there.

Step 1

Copy the address

https://mcp.biobam.com/engine

Step 2

Add it as a connector

In Claude: Settings › Customize › Connectors › Add custom connector. In Claude Science: Connectors › Remote connector. In ChatGPT: developer mode › Plugins › +.

Step 3

Sign in and approve

Sign in with your OmicsBox account, choose the subscription that pays for the analyses, and select Allow access.

Using Claude Code? One command:

claude mcp add --transport http omicsbox https://mcp.biobam.com/engine

Step-by-step guide for every assistant

Your data stays in OmicsBox

Inputs and results stay in your OmicsBox cloud storage. The assistant works with file names and cloud paths, and you can disconnect it at any time from Settings › Connected apps in OmicsBox Web.

No extra charge to connect

Analyses use Cloud Units from the subscription you choose, just like analyses launched from OmicsBox Desktop. Any charges for the assistant itself depend on your plan with its provider.

What you need

An OmicsBox account, an active OmicsBox subscription to run analyses, and an assistant that supports custom connectors.

Early Access program

Join the OmicsBox Engine Early Access program

Tell us how you want to use OmicsBox with AI agents, and we will keep you up to date on new capabilities as they become available.

Join Early Access AI at BioBam: OmicsAI

Documentation

OmicsBox for AI Agents · Connect Your AI Assistant · OmicsBox Engine CLI