Changes and updates in BiGGEsTS v1.0.4 (previous was 1.0.3)

- Fixed a MacOS specific problem which caused the text in the nodes of the Gene Ontology graph to not be displayed. This occured at least with Java 5.0. A flag was added to the JVM initialization in biggests.sh file: -Dapple.awt.graphics.UseQuartz=false. We recommend launching BiGGEsTS always via the script biggests.sh.
- Added "Export as text" functionality, accessible via right-click on the nodes in the tree holding matrices, biclusters and groups of biclusters. Several formats are available for biclusters and groups of biclusters. Check the manual.
- Graphviz for MacOS is no longer included in the distribution. Similarly to Linux users, MacOS users will have to install Graphviz prior to using BiGGEsTS.
- Fixed problems with the download of Gene Ontology files from the GO's FTP server. Ontology file is now downloaded via HTTP and the annotation files are downloaded from the CVS repository.
- Updated the list of organisms and corresponding ontology and annotation files.
- Fixed abnormal behavior of the application when adding the node to the tree after applying preprocessing techniques, in particular logarithmic transformation, before discretization.
- Removed hierarchical clustering functionality. This is no longer accessible, as it didn't make much sense in a biclustering analysis software.
- Updated Batik version (from 1.6 to 1.7), the Java SVG Toolkit used in BiGGEsTS to manipulate and display the graph of Gene Ontology terms.

Notice: The source of the (smadeira.*) package is available upon request. The .class files are available as a third-party library Biclustering.jar.