chem-bla-ics

CompLife'06 started today in Cambridge, UK. About 80 people are attending the meeting, and topics range from systems biology to QSAR. This evening there was a free software session mostly focussing on opensource software. Twelve projects were presented, among which the CDK (by me) and Bioclipse (by Ola), in five minute presentations, and a two hour demo period during a reception (free speech and free beer :). We had our brand new fliers with us, as well as a large poster for some additional branding.

One research presentation compared a number of fingerprint implementations in a QSAR study, and CDK came out very well, beating a few commercial programs. The free software session was full of CDK, however, with AMBIT, iBabel, Bioclipse and KNIME mentioning the CDK.

Day 5 was formally the last day (see also the summaries of day 1, day 2 and day 3/4) of the Chemistry Development Kit Bug Squash Party (BSP). Miguel uploaded the last bits of his CDK PDBPolymer to CML to CDK PDBPolymer roundtripping functionality (closing a bug and a feature request in one go). Have not tested this first hand yet, but looking forward to playing with this bit of code.

Because I was struggling hard with default values for cdk.interfaces fields, I did not have time to write up the Bug Squash Party report for day 3 (see also day 1 and day 2). But here it is.

Day 3

Kai worked hard on getting the cdk.interfaces API cleaned up, as agreed upon earlier. Christian added a test for the RMSD calculator (see getAllAtomRMSD()), and cleaned up his code a bit. Stefan continued his bug-squashing on JChemPaint and fixed another one or two bugs.

Like yesterday I will give short overview of things done at the Chemistry Development Kit Bug Squash Party (BSP). I think Stefan was the only to fix and close a bug report yesterday. Rajarshi added the MDE descriptor (yes, during a BSP new code might be commited too ;)

More interestingly, discussion on the developers mailing list on the patch by Todd Martin of the EPA to address deducing bond orders in

SMILES parsing (the major source of current open bugs!).

I plan to do a daily coverage of the Chemistry Development Kit Bug Squash Party (BSP). While Stefan was working hard to get the wiki machine back online after a hard-disc crash, Rajarshi, Miguel and me have been working hard. Miguel started to work on missing JUnit tests for bugs reported on SourceForge and Rajarshi fixed PMD, JavaDoc and other problems. I wrote 19 new JUnit tests and fixed two bugs, but with 44 bugs still open at SourceForge, there is quite some work to do.

There are a number of links I wanted to blog about, but never really had time for yet. Here's a short review of a them. Bio::Blogs is a series of summary/review articles of bio related blogs, and definately worth putting in your aggregator. Maybe someone is interested in setting up a Chemo::Blogs for chemistry blogs?

My del.icio.us (social bookmarking) network informed me about HTML Slidy, an XHTML based PowerPoint replacement.

Some time ago I blogged about the ChildResourceCreator extension point in Bioclipse and hinted as using that for PDB files. which contain 3D molecular models, sequences and bibliographic information. Using the new extension point, Bioclipse now treats PDB files as complex documents, creating child resources for the 3D molecular model (using the CDK plugin), and a sequence resource (using the BioJava plugin).

Bernard Munos at Eli Lilly & Co. wrote up a lengthy analysis on open source in drug discovery in Nature Reviews Drug Discovery: Can open-source R&D reinvigorate drug research? (DOI:10.1038/nrd2131). When scanning the article I saw this quote:

Other tools such as eMolecules, Jmol or the Chemistry Development Kit are adding powerful chemical search and visualization capabilities to the open-source scientist's toolbox.

Martin Szugat reported that a beta for BioJava 1.5 has been released. New features include: a new biojavax package with extension on the basic functionlity, such as the RichSequence.IOTools and the RichSequence object; a genetic algorithm library; features that allow manipulation of 3D structure files and objects; and non-HMM implementations of the NW and SW alignment algorithms.