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.

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.

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.

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!

Earlier I already reported that student text books were picking up Jmol as 3D viewer. Now, Nature Structural & Molecular Biology reports (DOI:10.1038/nsmb0206-93) that they picked it up too, using FirstGlance in Jmol (thanx Peter, for reporting this on the Blue Obelisk mailing list!). And, thanx Eric, for acknowledging the hard work of the Jmol developers.

This weekend I continued my work on getting the CDK and Jmol run with free, open source JVMs. Really, a lot works fine, as reported earlier in this blog: JChemPaint works and Jmol almost works (see the Classpath’s FreeSwingTestApps wiki page), and well over 95% of the CDK JUnit tests run without trouble too. So it comes down to identifying what does not run properly, and file bugs for this. For example, 26101 and 26108.

Today I received news on the Jmol user list that Lubert Stryer’s Biochemistry replaced the proprietary Chime with the open source Jmol. The third edition from which I learned biochemistry in my first year at the university did not feature a CD with live figures, but I am very thrilled to see a program on which I have actively programmed hit a text book I used myself in the past.

Where I was able to mention earlier that JChemPaint now runs with free (as in open source) Java virtual machines, I just tried to run the core Jmol renderer, using the Integration.java which comes as an example. Sadly, the original screenshots got lost there were made with jamvm 1.3.3 and classpath 0.19. It is very slow, however. I have not tried it with other free virtual machines, which are supposedly faster.