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Requirements

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 1.6 or newer. You can download Java for free from Oracle. ErmineJ will probably not work well on computers with less than 2Gb RAM (it can use 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.data. ErmineJ will also create a settings file in your home directory called ermineJ.properties, 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.

If you use ermineJ, we strongly recommend that you subscribe to the ermineJ users mailing list. This gives you the fastest access to information about updates as well as providing us with a type of “registration” to help us measure the number of users of ermineJ.

Run ermineJ now with Webstart

The easiest way to run ermineJ. Click here to start the software.

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-3.0.2-setup.exe
Mac OSX application package ermineJ-3.0.2-app.zip
Generic bundle ermineJ-3.0.2-generic-bundle.tar.gz
Source code ermineJ-3.0.2-src.tar.gz

ErmineJ is free software; see the license details.

Gene Annotation files

To use the software, you need gene annotation files and a Gene Ontology XML 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.

Additional annotation files can be downloaded from here. Copy them somewhere you can find them (e.g. in your ermineJ.data directory). It is not necessary to unzip them. You may also use Affymetrix or Agilent supplied files. 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). For gene-disease relationships we suggest Phenocarta, which provides files for human and mouse.

Installation

On MS Windows 8/Vista/7/XP, simply run the installer and follow the instructions.

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

Note: For MacOSX 10.8 or higher, the application bundle currently does not have an Apple certificate, as a result, you may get an error that the application is damaged when starting the program. You can tell the operating to system to run applications without a certificate by setting  System Preferences > Security & Privacy > General > Allow apps downloaded from: Anywhere. Alternatively, you may run the bin/ermineJ.sh script instead (see the installation notes for details).

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.

Example

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.