OmicsBox Engine
Run OmicsBox from your terminal, your pipelines, or your AI assistant
The OmicsBox Engine brings the analyses of OmicsBox to the command line and to AI assistants such as Claude and ChatGPT. Same tools, same account, same cloud storage as OmicsBox Desktop and OmicsBox Web.
Two ways to work with the Engine
Script OmicsBox for reproducible pipelines, or let your AI assistant run analyses for you. Both use the same OmicsBox tools on OmicsCloud.
Early Access
Command line
Nextflow
Snakemake
OmicsBox Engine CLI
Run OmicsBox analyses from a terminal, on a server or inside a container, and integrate them into workflow managers such as Nextflow, without opening the graphical interface.
- Reproducible, scripted and versioned analyses
- The same tools and parameters as OmicsBox Desktop
- Detach long cloud jobs and reconnect later with a run ID
- Linux and Windows packages
omicsbox list
omicsbox describe deseq2
omicsbox deseq2 [options] --detach
Available now
MCP
Claude
Codex
Gemini
OmicsBox for AI Agents
Connect your AI assistant to OmicsBox and ask for analyses in everyday language. The assistant finds the right tool, runs it on OmicsCloud and gives you a link to open the results in OmicsBox Web.
- Works with Claude, ChatGPT, Claude Code, Codex, Cursor and VS Code
- No code, no installation, no API key to copy
- “Run a differential expression analysis with DESeq2 on counts.txt, comparing treated and control samples.”
https://mcp.biobam.com/engine
One account, one subscription, one cloud
Every way of using OmicsBox shares the same account, subscription and cloud storage. Start an analysis from your terminal or your assistant, then open the result in OmicsBox Web or OmicsBox Desktop.
Desktop
Explore data and inspect results interactively on your computer.
Web
Open, review and share results in your browser. Nothing to install.
Engine CLI
Automate analyses in scripts, servers and pipelines.
AI Agents
Ask your AI assistant to run and explain analyses for you.
How to get the Engine
The Engine is part of your OmicsBox subscription. It is added as a module alongside the analysis modules (Functional Analysis, Transcriptomics, Genome Analysis, Genetic Variation and Metagenomics), so there is no separate product to buy. The CLI is currently in Early Access: join the waitlist and we will contact you as soon as it is ready for you.
Early Access program
Join the OmicsBox Engine waitlist
Tell us how you would like to use the Engine, in pipelines, on servers or with AI agents, and we will get in touch when the CLI is ready for you.