chem-bla-ics

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. But open source software development, at least in chemistry, needs funding, because there are too few people working on such software on a voluntary basis.

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. Unfortunately, he discusses free, but closed source, program in one go.

He discusses the advantages and problems with opensource, and mentions the often lacking user-friendly GUI (true), and the the lack of literature to validate the program.

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.

After Kalzium and kfile_chemical, KDE has now be extended with kparts for 3D structure and spectrum display: Kryomol. It is written in C++ and licensed GPL. It supports several chemistry formats, among which quantum chemical formats like Gaussian03, NwChem and ACES, and 3D structures as MDL molefile and XYZ.

With quite some help from Ola (thanx!), I made good progress with the CMLRSS plugin. The current result looks like:

A problem in the transition from Jumbo 5.0 to 5.1 is causing a problem so that it does not show a 3D model or 2D diagram, but that will follow soon.