ErmineJ is stand-alone (desktop) software. It does not run in a web browser. All data and analysis results remain on your computer and are not uploaded anywhere.

ErmineJ requires Java 8 or newer. You can download Java for free from Oracle (select the 64 bit version). ErmineJ will probably not work well on computers with less than 4Gb RAM (it can use over 1Gb of RAM). ErmineJ requires an internet connection to be able to automatically fetch annotation files, but otherwise will work fine “offline”.

ErmineJ will save files to your computer’s hard drive, by default in your home directory in a directory called ErmineJ will also create a settings file in your home directory called, and will produce a log file called ermineJ.log. The log file is a just a text file and contains information useful in case of problems with the software.

Run ermineJ now with Webstart

The easiest way to run ermineJ. Click here to start the software. You will need to have Java installed already.

If you want to install ErmineJ “locally”, see the next sections. Otherwise, instructions on getting started can be found here.

Software Files

Description File
Windows installer ermineJ-3.2-setup.exe
Mac OSX application package ermineJ-3.2.dmg
Generic bundle ermineJ-3.2-generic-bundle.tar.gz
Source code ermineJ-3.2-src.tar.gz

ErmineJ is free software; see the license details. Fork it on GitHub.

Gene Annotation files

To use the software, you need gene annotation files and a Gene Ontology OBO file. As of version 3.0, you can get these from within the software, so we recommend simply running the software and seeing if what you need is already provided. XML support was dropped in version 3.2 as the format ermineJ used is no longer supported by the GO consortium. If you need to re-run old analyses that use the XML format, download an older version of ermineJ such as 3.1.2 (generic bundle here).

Additional annotation files can be downloaded from here. Copy them somewhere you can find them (e.g. in your directory). It is not necessary to unzip them. If you have your own annotations in a format that is not supported, let us know. Note that we provide “generic” (gene-based) annotation files for some organisms (those supported by Gemma), keyed by gene symbols, Entrez Gene IDs, or Ensembl Gene IDs; you don’t need to be using a microarray.

You can also define your own gene sets using ermineJ or import them into ermineJ. For example, in this manner ErmineJ supports the use of MolSigDb “GMT” files (gene symbol version).


On MS Windows, simply run the installer and follow the instructions.

On Mac OSX, unpack the .dmg file and drag the resulting “ermineJ” application bundle to your Application directory.

For other platforms (e.g. Linux), if you don’t want to use Webstart, you should be able to use the “Generic bundle”. There is a README file included that gives some instructions. The Generic bundle is also appropriate for command-line users of ErmineJ.

For more help with installation see this page, or this page.

Once you have ErmineJ installed, go here to get started.


If you don’t have your own files yet and want to see what the software does, we provide the following which use the venerable GPL91 (Affymetrix HGU95Av2) expression profiling platform. You can get the GPL91 annotation file from within the software or download it directly here.

ermineJ-exampleScores  – “Gene scores”, which are p-values for a differential expression analysis

ermineJ-exampleData – Gene expression profiles.