Bioclipse is a free and open source workbench for the life sciences. Bioclipse is based on the Eclipse Rich Client Platform (RCP) which means that Bioclipse inherits a state-of-the-art plugin architecture, functionality, and visual interfaces from Eclipse, such as help system, software updates, preferences, cross-platform deployment etc. Cheminformatics in Bioclipse is mainly based on the Chemistry Development Kit (CDK), and contains a framework for managing and analyzing chemical compounds. Bioclipse supports editing in 2D, processing large collections of molecules in tables, calculation of various types of properties, and much more cheminformatics functionality. The Jmol application is integrated in Bioclipse as an editor, and provides advanced interactive 3D visualizations. Bioinformatics in Bioclipse concerns primarily the management and analysis of biological sequences (DNA, RNA, and protein). Bioinformatics in Bioclipse relies heavily on BioJava, which provides core bioinformatics functionality, and a graphical editor for sequence alignments. Various clients for Web services are also available to facilitate downloading of e.g. biological sequences and annotations, as well as for bioinformatics analysis.