About Bioclipse

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.

Bioclipse provides advanced functionality in fields such as cheminformatics, bioinformatics, semantic web, spectrum analysis, drug discovery, safety assessment, and general chemistry education.


Bioclipse is developed as a collaboration between the Proteochemometric Group , Dept. of Pharmaceutical Biosciences, Uppsala University, Sweden, and the Cheminformatics and Metabolism Team at the European Bioinformatics Institute (EBI).

Bioclipse is released under Eclipse Public License (EPL) + exception, see the License Statement, putting no constraints on choice of backend and/or license for creating plugins for Bioclipse; it is totally open for both open source plugins as well as commercial.

If you use Bioclipse in your research, please cite:

Bioclipse: An open source workbench for chemo- and bioinformatics
Ola Spjuth, Tobias Helmus, Egon L Willighagen, Stefan Kuhn, Martin Eklund, Johannes Wagener, Peter Murray-Rust, Christoph Steinbeck, Jarl E.S. Wikberg
BMC Bioinformatics 2007, 8:59          doi:10.1186/1471-2105-8-59            Fulltext


Bioclipse 2: A scriptable integration platform for the life sciences
Ola Spjuth, Jonathan Alvarsson, Arvid Berg, Martin Eklund, Stefan Kuhn, Carl Mäsak, Gilleain Torrance, Johannes Wagener, Egon L Willighagen, Christoph Steinbeck and Jarl ES Wikberg
BMC Bioinformatics 2009, 10:397      doi:10.1186/1471-2105-10-397        Fulltext


See also articles citing Bioclipse.



The Bioclipse Team would like to thank the following companies for sponsoring the development of Bioclipse:

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