Installation of J-Express

Here we will give a point-for-point instuction on how to install J-Express to your laptop.


  1. Make sure you have Java version 6.0 installed on your laptop. See
  2. For a client-admin (klient-driftet) PC you have several options
    1. J-Express installed on your laptop by the IT-department at your workplace. Make sure your installation still pass the tests mentioned further down.
    2. Install and run the program from an Administrator-account on the laptop.
    3. Install and run the program from an area of your PC you have full access to (i.e. physically located on the laptop, like D:\J-Express. Do not install it in your home directory or a network drive that is mounted/syncronized over the network)
  3. For PCs where the user has full access to both installing and running programs, use the multiplatform installer to  install the program.


For option 2B), 2C) and 3), download and use the setup.jar multiplatform installer file from the Download section of



Once the program is installed, you can add the full license package, which is free for all academic users in Norway. To get the license send an e-mail to with your full name, e-mail address and organization affiliation, and you will get the license key with instructions on how to add it to the program in an e-mail. For other users, a license can be purchased from You will need the full license package for this course.



 After installing the program and adding the license package, do the following test to see if the program works properly. This is very important, as we don’t have time for debugging during the course. Use the test-dataset provided with the program. You find this in the data-folder installed together with J-Express.

1.       Start the program from the Start menu (or double clicking the Launch.jar file in the J-Express folder)

2.       Open the file using “File | Load project” from the main menu bar and navigate to the “J-Express/data” folder.

3.       Click to highlight the “Diauxic shift” dataset in the top left window named “Project” (expand the project by clicking on the icon in front of the “Test Project” name if the “Diauxic shift” dataset is not visible)

4.       Start an analysis on the selected dataset by selecting “Method | Clustering | Hierarchical clustering” from the main menu.

5.       Just click “OK” to accept default parameters

6.       You should now get a new window with a heatmap (coloured rectangle) representing the clustering of the gene profiles and sample columns in the dataset.

 If you have problems getting the program to work as it should, please contact Solveig M. Olafsrud ( who will assist you in finding the reasons for  the problem.