On behalf of all Bioclipse developers I am happy 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.
Figure 1: Screenshot of Bioclipse showing editing of a chemical structure using the new JChemPaint editor.
Bioclipse is a Rich Client for the life sciences that provides the means to run and integrate algorithms and tools in disconnected state, while still taking advantage of remote services if a network connection is available. Built on the famous Eclipse framework, Bioclipse delivers a state-of-the-art plugin architecture which makes it possible to extend it in any direction.
Figure 2: Screenshot of the interactive 3D visualization of a protein using the integrated component Jmol.
Bioclipse 2 can be downloaded from Sourceforge, releases are available for all major platforms. There is an update site where users can install additional functionality (such as Speclipse) and data collections; this is available from the Bioclipse workbench under menu Help > Software updates.
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 mailing list.
All software contains bugs, and Bioclipse is no exception. However, in contrast to many commercial and closed source initiatives, open source projects generally have a faster bug fixing rate as well as more frequent releases. If you find bugs in Bioclipse, please report them on bugs.bioclipse.net. There is a list of intractable bugs on the Bioclipse development wiki, and also a convenience list for tracking known major bugs.
Bioclipse is an open development that welcome new developers with varying backgrounds. Developers hang out on daily basis on IRC (irc.freenode.net, channel #bioclipse), and can also be reached via the mailing list bioclipse-devel.
Thanks to all contributors who made this release possible!