We are also developing GenePath, a program for discovery of genetic regulatory networks from experimental data. Check GenePath's site and run the software on web!
Source code for FreeView and FreeOView is available under the condition that if you use it and publish the results, our original contribution should be cited as:
Marko Kavcic, Blaz Zupan: FreeView, http://www.ailab.si, University of Ljubljana, Slovenia, and Baylor College of Medicine, Houston, TX.
Java and other files that form Free(O)View are available as a ZIP file. A source code documentation as produced by javadoc is available.