Download and installation

Requirements

ermineJ requires a Java 2 Runtime Environment (JRE) 1.5 or newer to run. You can download the platform-specific packages from SUN's website ( http://java.sun.com/j2se/ ). Users of MS Windows NT/2000/XP can alternatively download the Windows installer with bundled JRE package below. On machines with less than 256 Mb of RAM ermineJ may suffer from poor performance.

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

You can run ermineJ from any operating system that supports Java without running the installer by using java webstart.

If you have Webstart installed, you run ermineJ right now. If you don't have Webstart, get it here.

Mac users should use webstart to install ErmineJ. The Mac OS will ask you if you would like to create a "shortcut" so that you don't have to use webstart again. Currently this is the only way of installing ErmineJ on the mac.

Software Files

The standard bundle includes a GO XML file and two sample microarrray annotation files for mouse and human Affymetrix microarrays. See the "Annotation files" for information on how to get other annotation files.

Annotation files

To use the software, you have to have microarray annotation files and a recent Gene Ontology XML file.

Go here to get microarray annotation files.  Copy them somewhere you can find them. It is not necessary to unzip them. You may also use Affymetrix or Agilent supplied files.

ErmineJ is distributed with a recent GO XML file (except the 'lite' version). If you want to get a newer one, go here to get the XML file ( go_daily-termdb.rdf-xml.gz ), found here. It is not necessary to unzip the file.

Note that you can also define your own gene sets using ermineJ or import them into ermineJ.

Installation

Perhaps the easiest way to run ermineJ is by using webstart, but it can be installed manually. Note that no GO or microarray annotation files are distributed with the webstart version.

On MS Windows NT/2000/XP, simply run the installer. For earlier versions of windows, you should use the "Generic bundle"

For other platforms, you should be able to use the "Generic bundle". There is a README file included that gives some instructions.

For more help with installation see this page.