The data classes of the Chemistry Development Kit are mutable, unlike those of Octet. This means that other classes may need to respond when the content updates. For example, a render class. CDK’s ChemObject provides a notifyChanged() and addListener() methods for this.

Bioclipse 1.0 is to be released in May, and the cartoon on script command is still not working in the Jmol viewer. For those who do not know yet, Bioclipse is a cool Eclipse RCP based Java chemo-and bioinformatics workbench. To have a better idea what goes on inside Bioclipse, I wrote a new BioPolymer tree to show me the strands in the protein.

The Self-organizing map (SOM) is a popular (again) and intuitive non-linear mapping method: it transforms a multidimensional space into two dimensions (normally: they are so easy to visualize). Latino and Aires-de-Sousa published a paper that uses this method to analyze the whole KEGG pathway database: Genome-Scale Classification of Metabolic Reactions: A Chemoinformatics Approach (DOI: anie.200503833). The method is based on earlier

Internet has the nice feature of bringing together people. This has helped many open source projects in the past. But it is also a convenient and cheap way to have conferences. Next month, the ChemConf 2006 conference will be held, and interested people only need to subscribe to a mailing list to participate. The topic of this years ChemConf is Web-Based Applications for Chemical Education.

While I was working on implementing proper author-given chain IDs in PDB structures for Jmol’s mmCIF reader today, I thought it was interesting to mention the recent article Traditional Biomolecular Structure Determination by NMR Spectroscopy Allows for Major Errors by Nabuurs (DOI:10.1371/journal.pcbi.0020009, open access), working at the CMBI, two floors away from my former working location at the Radboud University Nijmegen.

An InChI (or see the FAQ) is a line notation for a molecular structure that was recently developed by the NIST and the IUPAC. Principally they can be applied to protein too (see below), but because proteins would give lenghty InChI’s and are quite well defined in terms of connectivity anyway, those can better be described by their amino acid sequence.

As of April 3, I will be working as postdoc in the group of Christoph Steinbeck at the Cologne University BioInformatics Center, or simply CUBIC, for a year. Though no exact plans have been decided upon, the work will include CDK, CML, ontologies, Bioclipse, semantic web technologies, Jmol, and other interesting things. Research areas will at least include QSAR, but I hope to touch bits of bioinformatics too.

Dan (the original Jmol author) has an interesting blog series: How to make money from Open Source scientific software I, II and III. Three more blog items are in the planning. The deal with how to make money from open source scientific software. He wants to be able to skeptically review the software in his field, hence open source.

The beta has been using Jmol as one of the viewers for ages already, but this beta is no longer: it’s the new interface for the PDB database.

Geldenhuys et al. published an article in Drug Discovery Today titled Optimizing the use of open-source software applications in drug discovery (DOI:10.1016/S1359-6446(05)03692-5), and approached the review from a bench chemist point of view.

A few days back, Classpath 0.90 was released, the first release after the 0.20 release. Earlier Classpath releases could run the rendering engine , but running the application failed so far . Today it hit Debian unstable, so upgrade my sid32 chroot and had Cacao run Jmol. I had some memory issues opening a small molecule (4-methyl-2-pentyne), and the rendering speed was a factor 100 or so slower than Sun’s JVM, but it runs!