Presenting at Society of Toxicology 2011

Tomorrow I will present a poster at the Society of Toxicology Annual Meeting 2011 in Washington DC. With over 7,500 participants, this conference is rather large. My poster has the title: "A flexible method for building and using predictive models applied to safety endpoints" and mainly described the Decision Support feature for Bioclipse. Anyway, this is what my poster looks like:

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:

• Download Bioclipse 2.2.0.
• Bioclipse help (online version)
• Bioclipse website
• Bioclipse 2.0 announcement
• Installation guide
• Report a bug
• Mailing lists

Bioclipse 2.0 released

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.

All functionality in Bioclipse 2 is available from the GUI as well as a new scripting language based on Javascript. This allows for complete control of the workbench and functionality from scripts, which can be used to automate tasks or reproduce and validate scientific analyses.

Figure 3: All functionality in Bioclipse is available from an integrated scripting language based on Javascript.

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!