Bioclipse: an open source workbench for chemo- and bioinformatics

Bioclipse is an advanced workbench for resources in chemo- and bioinformatics, such as molecules, proteins, sequences, spectra, and scripts. It provides 2D-editing, 3D-visualization, file format conversion, calculation of chemical properties, and much more; all fully integrated into a user-friendly desktop application. Editing supports standard functions such as cut and paste, drag and drop, and undo/redo. Bioclipse is written in Java and based on the Eclipse Rich Client Platform with a state-of-the-art plugin architecture. This gives Bioclipse an advantage over other systems as it can easily be extended with functionality in any desired direction.Bioclipse is a powerful workbench for bio- and chemoinformatics as well as an advanced integration platform. The rich functionality, intuitive user interface, and powerful plugin architecture make Bioclipse the most advanced and user-friendly open source workbench for chemo- and bioinformatics. Bioclipse is released under Eclipse Public License (EPL), an open source license which sets no constraints on external plugin licensing; it is totally open for both open source plugins as well as commercial ones. Bioclipse is freely available at http://www.bioclipse.net webcite.Chemo- and bioinformatics are important and active research areas with an ever-increasing number of algorithms and software implementations. Numerous applications provide functionality for highly specific tasks, but very few provide a complete one-package solution where all functionality is integrated into a user-friendly workbench. Commercial software like MOE (Chemical Computing Group) and Discovery Suite (Accelrys) contains a lot of features, but are expensive applications, and generally do not allow unlimited extensibility, or have restricted access to source code.Existing open source projects in bioinformatics that try to solve this problem are usually focused on integrating existing software applications. Jemboss [1] wraps around the EMBOSS [2] collecti