Bioclipse: an open source workbench for chemo- and bioinformatics

Abstract

Background: There is a need for software applications that provide users with a complete and extensible toolkit for chemo- and bioinformatics accessible from a single workbench. Commercial packages are expensive and closed source, hence they do not allow end users to modify algorithms and add custom functionality. Existing open source projects are more focused on providing a framework for integrating existing, separately installed bioinformatics packages, rather than providing user-friendly interfaces. No open source chemoinformatics workbench has previously been published, and no successful attempts have been made to integrate chemo- and bioinformatics into a single framework.

Results: 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.

Conclusion: 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.

Figure 1

Plugin dependencies. Overview of the plugin dependencies for Bioclipse.

Figure 2

Object model. Class diagram of the object model in Bioclipse. Plugins contribute BioResources at runtime using extension points.

Figure 3

Screenshot of the Chemoinformatics Perspective. The Chemoinformatics Perspective showing the BioResource Navigator (on the left), JChemPaint editor with a 2D diagram of ATP (middle), Console echoing messages to the user (bottom), ChemTree view with the atoms and bonds (top right), and the Properties view displaying properties for the selected molecule (bottom right).

Figure 4

Screenshot of the Bioinformatics Perspective. Structure of the protein 1d66 retrieved via an EBI webservice [25]. The BioResource Navigator (on the left) shows a 3D structure and an amino acid sequence object. Selecting residues in the sequence view (bottom) highlights the corresponding structural features in the Jmol view (right).