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Bioclipse 2.2 released

The Bioclipse Team is proud to announce the release of Bioclipse 2.2.0. The new version includes, apart from numerous bug fixes, the following highlights:

Cheminformatics, with a pure SWT-based chemical 2D editor (JChemPaint) and a lazy-loading molecules table.
QSAR, supporting local, REST, and XMPP services
MetaPrint2D for interactive site-of-metabolism prediction for chemical structures
StructureDB and VScreen: A chemical database with virtual screening functionality
The new Decision Support feature with graphical reports using BIRT
Semantic web features
Bioinformatics, with the new Sequence Editor and sequence alignments via the Kalign Web service (Experimental)

A screenshot from Bioclipse with the MetaPrint2D feature showing predicted sites of metabolsim for a set of drugs in the MoleculesTable.

Note that Bioclipse 2.2.0 requires a fresh download, i.e. it can not be upgraded to by using the software update functionality. A small installation guide is also provided, but the main documentation for Bioclipse is available from help.bioclipse.net; the same information is also available from within Bioclipse from the menu Help > Help Contents. For general questions there is the bioclipse-users and bioclipse.devel mailing lists. Links:

Bioclipse development releases

Bioclipse is a large and fast moving project. Stable releases are available from Sourceforge, but new functionality might only be available from one of the recent Development Releases. Note that development releases may also include functionality which should be considered stable, but moving a release to Sourceforge requires much more testing, and is only done at certain intervals.

Bioclipse 2.0 released

We are proud to announce the release of Bioclipse 2.0. Bioclipse is a free, open source workbench for the life sciences that provides advanced functionality mainly in cheminformatics (bioinformatics is planned for version 2.1 later this summer). Some major components include a brand new chemical editor for SWT (JChemPaint), interactive 3D visualization of molecules (Jmol), a Molecules Table capable of reading large files, and a powerful backbone in cheminformatics provided by the Chemistry Development Kit (CDK) library.

Here is the full announcement.

Bioclipse awarded at Trophees du Libre

Ola Spjuth and Georg Greve

At the international contest for free software, Trophees du Libre, 2007 which was held in Soissons, France, Bioclipse was awarded the Special Prize of the jury. The prize was handed over by the president of the Free Software Foundation Europe, Georg Greve, who also was the chairman of the jury and gave the following motivation:
“Bioclipse is breaking new ground by integrating different research areas in life science and making the tools available as Free Software for everyone. It is the jury’s expectation that the project will have major impact in the future of life science research and education.”

Michel Lara, Program Manager at the Paris Innovation Center of IBM France and member of the Jury explains: "Bioclipse is an innovative project with high potential. The jury was completely united in the decision that Bioclipse should receive the Special Prize".

Bioclipse project leader Ola Spjuth represented Bioclipse on the occasion.

Bioclipse publication online

The Bioclipse project team is proud to announce that the Bioclipse article was published today in BMC Bioinformatics.

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 (22 February 2007)
[ Abstract ] [ Provisional PDF ]

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Bioclipse Workshop 2007

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