Installing and running j-express

Updates:
 

18.jul.2001	Version 2.0 available at http://www.molmine.com
16.aug.2000	Updated the PCA module.
20.aug.2000	Empty spaces in the dataset can be set to the average value in the dataloader. Empty spaces in the dataset are displayed by a red "NULL" string.  Added a horizontal scrollbar in the zoomed dendrogram window  Empty spaces are marked by blue dots in the dendrogram (main and zoomed). Problems in the SOM-visualisation with java 1.3 are fixed.  Ability to save gene identifiers and their expression values is added to the "save" button in the gene graph. CR characters are removed from the input data. These characters were visible as squares and caused problems in the last data column.
20.oct.2000	Fixed the problem with empty spaces in the fist or last column in the dataloader. Thanks to Philippe Marc for reporting this bug. Fixed a bug in the plotting of the principal components in the PCA module. Thanks to Martin Beibel for reporting this bug.

 

Installing and running

To run j-express, java runtime environment 1.2 or higher must be installed. This can be downloaded from www.javasoft.com. The file jexpress.jar must be unpacked either with jar, which is a standard java packing program and a part of the java runtime environment, or with regular zip/winzip. When this is done, it should be enough just standing in the directory with the cluster.class file and type "java cluster". If the data we're analysing is large, it can be necessary to use the -mx parameter to allocate more memory to the application. For example if we want the program to be able to use 100MB, we should run the program with "java -mx100M cluster". Remember that when using hierarchical clustering we calculate a distance matrix. If we analyse 6000 genes, we want to keep the distance between each gene to all the other genes, requiring a triangular matrix of 6000*6000 elements. If we allocate the memory to the matrix as integer values, the program will demand: (((6000*6000)/2)*32 bits)/8 bytes = 72MB just for the distance matrix.

Download Jexpress.jar here

Download Jexpress.zip here

Download Jexpress.exe here (Self extracting zip archive for Microsoft windows users)

Step by step:

1. If not installed, install the java runtime environment 1.2 or newer by downloading it from http://www.javasoft.com/products/jdk/1.2/jre/index.html, Mac users:http://developer.apple.com/java/text/download.html
2. Make a directory to install j-express.
3. Copy the jexpress.jar to this directory.
4. Unpack the jar file with: "jar -xvf jexress.jar" or "unzip jexpress.jar" (The exe-file can be double-clicked from microsoft windows). Renaming the jexpress.jar to jexpress.zip will make it a regular zip file.
5. Run the application with "java cluster" or "java -mx80MB cluster" (or another amount of memory(type java -mx for details))
6. Start analysing. A testfile can be found in the dataset directory.

1. From the MRJ SDK 2.2 folder, open the Tools folder
2. Then open the Application Builders folder.
3. Finally open the JBindery folder which contains the application JBindery.
4. Drag and drop the cluster.class file in the MRJ SDK 2.2 folder on top of the JBindery icon.
5. Click run on the appearing dialog.

Sollution to a common problem on macs: upgrading the Swing package:
This must be done when running J-Express results in this failure:
 

Exception Occurred:
java.lang.NoClassDefFoundError: javax/swing/JProgressBar
at cluster.<init>(cluster.java:57)
at cluster.main(cluster.java:66)
at com.apple.mrj.JManager.JMStaticMethodDispatcher.run(JMAWTContextImpl.java)
at java.lang.Thread.run(Thread.java)

Fix:

1. Go to the site http://www.ing.unitn.it/~luttero/javaonMac/
2. Find and download the swingall.jar file
3. unstuff it and drop the swingall.jar file into:

<:System Folder:>Extensions:MRJ Libraries:MRJ Classes (overwrite if nessesary, but back up the old file)
4. Now try running jexpress again. It should work.

you may also use this address to report bugs or contribute with new ideas.

See the help files for how to use the application and how the methods work.