I have heard that bioinformatics is ahead of chemoinformatics. However, I discoverd that this is not necessarily the case, while preparing for a homology modeling course I gave this week at the CUBIC. Open Access is really no issue there, with open access journals and many open access databases. But it is different when it comes down to open source software.

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.

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.

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.

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.

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?

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?

Chemical Archeology (see Christoph’s comment) is the process of extracting chemical information from old journal articles. Some time ago, Peter Corbett from the group of Peter Murray-Rust visited the CUBIC to talk to us about Oscar3 which can do just that. That day, we already hooked OPSIN into Bioclipse .

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.