The QSAR feature turns Bioclipse into a fully-fledge workbench for QSAR. It is fully QSAR-ML compliant, and there are several implementations of descriptor providers, for example CDK (local, REST, XMPP) and JoeLib (local).
Download one of the pre-built packages below and unzip on your local computer (Note that you need Java 1.5, Java 1.6 MIGHT work but is not supported).
The first thing to do is creating a new QSAR project. Do this from the menu File > New ... and select QSAR Project. Double-click the generated file qsar.xml to open the QSAR editor. Add some molecules, select descriptors, and hit the button "Calculate" in the top right corner of the QsarEditor. See the introductory screencast for a visual tutorial.
If you use Bioclipse-QSAR or QSAR-ML in your scientific projects, please cite:
Towards interoperable and reproducible QSAR analyses: Exchange of data sets
Ola Spjuth, Egon L Willighagen, Rajarshi Guha, Martin Eklund, Jarl ES Wikberg
Journal of Cheminformatics 2010, 2:5 doi:10.1186/1758-2946-2-5