The SOM viewing application is simply a collection of 3 perlscripts and a Perl module (which contains some common functions).
The three programs are:
  1. SOMview.pl
  2. makeCluster.pl
  3. makeEvo.pl
  4. ExImage.pm
To use these, all four programs must be placed in a cgi-bin directory on a web server, and if they are not already, must be made executable, using:

chmod +x SOMview.pl
chmod +x makeCluster.pl etc

To actually use the viewer, you must edit the files, to insert the names of some variables. You need to do this in all the files with a .pl extension. In all three cases you will see: 


#############################################################################################
#                                                                                           #
#          You need to define the following variables                                       #
#                                                                                           #
#          a trailing '/' character is required for each of them                            #
#                                                                                           #
#############################################################################################

$tmpDir= ""; # html tmp directory where you want to save the images
$dir   = ""; # the directory where the .cdt and .som files exist
$link  = ""; # the base url of the html tmp directory

#############################################################################################

near the top of each program. You need to fill in these variables, based on where the correct locations are on your system. If you don't know, or don't understand, then I can't offer help. You'll have to ask your system administrator.
For the scripts to work your system will have to have Perl installed (at least 5.004), and recent versions of both the GD and CGI modules, which are available here. Note my scripts were written when using a version of GD that created gif images. If you have the latest versions, which produce png images, it may not work. I have not done any testing with the latest GD module, so you'll have to figure it out yourself. To actually view a SOM, you'll have to create one first, using my clustering program. You'll need to make sure that all the files output by the program are put into the correct directory ($dir) as specified above. You then need to go in your web browser to:

http://YOUR_SERVER_NAME_HERE/cgi-bin/SOMview.pl?stem=YOUR_STEM

The stem is determined by what type of cluster you made. For instance if your input file name to the clustering program was sample.txt, and you asked for a 3 x 6 SOM, then the stem would be sample_3_6, whereas if you asked for a k-means cluster, with 10 clusters, then the stem will be sample_10. The SOMview.pl program will determine whether that corresponds to a SOM, or a k-means cluster, the create a table to view the results accordingly. The images within the table are clickable, so that you can zoom in a view the genes that make up each cluster.
The software is freely available to all researchers from non-profit and academic institutions (upon signing of a license agreement, available as a Word document here. Please fax back the completed license agreement to 650 723 7016, directed to the attention of Gavin Sherlock, indicating your email address).