BiomiX 3.0 — Now available

Multi-omics integration
for every researcher

A graphical desktop platform that makes state-of-the-art multi-omics analysis accessible without programming expertise.

5
Integration methods
3
Omics layers
0
Lines of code required

What's new in BiomiX 3.0

Built on the same GUI philosophy, now with broader integration capabilities and simpler deployment.

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4 new integration methods

SNF, NEMO, DIABLO, and PRAMIGO join MOFA to offer unsupervised, supervised, and graph-based strategies in a single interface.

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Docker-based installation

No more manual dependency management. BiomiX 3.0 ships as a Docker container for a reproducible, one-command setup across all platforms.

Nextflow pipelines

Run scalable, reproducible analyses through integrated Nextflow workflows — from laptop to HPC cluster.

Everything you need, in one interface

Biological interpretation

Automated biological interpretation

Once your integration is complete, BiomiX automatically runs pathway enrichment via EnrichR and retrieves relevant PubMed literature for each identified factor or component — turning statistical results into biological insight with a single click.

Multi-omics integration without coding

Multi-omics integration without coding

Five state-of-the-art integration methods — MOFA, SNF, NEMO, DIABLO, and PRAMIGO — are all accessible through the same graphical interface. No R, no Python, no command line. Just your data and your question.

BiomiX community and stability

Built to last, backed by a community

BiomiX is an open-source project actively maintained by a multi-institution European consortium. Docker-based deployment guarantees that your analyses remain reproducible regardless of system updates, while an active developer and researcher community ensures the platform keeps growing.

Meet the team →

Single-omics analysis, just a click away

Customizable pipelines for transcriptomics, metabolomics, and methylomics. Choose your parameters and let BiomiX handle the analysis — so you can focus on the biology.

Single-omics pipeline overview
Single-omics results example

Five integration strategies, one platform

Choose the method that fits your question — or run them all and compare.

MOFA
Unsupervised · Factor analysis
SNF
Unsupervised · Network fusion
NEMO
Unsupervised · Partial overlap
DIABLO
Supervised · Sparse CCA
PRAMIGO Soon
Supervised · Graph transformer
Explore integration methods →

Up and running in minutes

BiomiX 3.0 installs via Docker — no dependency conflicts, no configuration.

# Pull and run BiomiX 3.0
docker pull ghcr.io/biomix-consortium/biomix:3.0
docker run -p 8080:8080 \
  -v /path/to/your/data:/data \
  ghcr.io/biomix-consortium/biomix:3.0

Supports Linux, Windows, and macOS. Full instructions on the Installation page.

Cite BiomiX

If you use BiomiX in your research, please cite our publication in BMC Bioinformatics. A manuscript describing BiomiX 3.0 is currently under review.

Read paper (v1) ↗
Iperi C. et al. BiomiX, a user-friendly
bioinformatic tool for democratized analysis
and integration of multiomics data.
BMC Bioinformatics 26, 8 (2025).
doi: 10.1186/s12859-024-06022-y