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STATegraEMS, the Experiment Management System

STATegra EMS is an Experiment Management System (EMS) for omics experiments that supports different types of sequencing-based assays, proteomics and metabolomics data. We specifically support experiments such as RNA-seq, miRNA-seq, Chip-seq, Methyl-seq, or DNase-seq and can easily be extended to support additional sequencing assays. The system has been developed to provide research laboratories with an integrated system that offers a simple and effective way for experiment annotation and tracking of analysis pipelines from raw data to ready-to-use measurements, using free, open source software technologies.

STATegra EMS has been developed by the Genomics of Gene Expression Lab at Príncipe Felipe Research Centre.

Cite us

STATegra EMS was published at BMC Systems Biology on March 2014, you can find an open-access version for the article here.

  • Citation:

Hernández-de-Diego R, Boix-Chova N, Gómez-Cabrero D, Tegner J, Abugessaisa I, and Conesa A. STATegra EMS: an Experiment Management System for complex next-generation omics experiments. BMC Syst Biol. 2014;8 Suppl 2:S9. doi: 10.1186/1752-0509-8-S2-S9.

How to install

Since version 0.6, the STATegra EMS includes an auto-installer script which makes easier to deploy and configure the the system. Please visit the STATegra EMS documentation for more information.

Docker for STATegra EMS

The STATegra EMS Docker Image is an easy distributable full-fledged STATegra EMS installation. Using dockers you can easily deploy your own instance of STATegra EMS in few seconds. Read more


A complete documentation is available at the readthedocs platform.


Rafael Hernández de Diego, Main Developer,

Ana Conesa, PhD., Head Genomics of Gene Expression Lab.

For any question on STATegraEMS, users can send a mail to