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

Earlier I reported about postgenomic.com , and needed some diversion from my manuscript work (could no longer think straight about the article I’m working on). So time for some reading up on new technologies. Timing was perfect, because the source code of postgenomic.com got just uploaded to SourceForge SVN.

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.

For the past few weeks I have been working on a review article, which will contain a section with new QSAR/QSPR descriptors published in the period 2000-now.

OpenSource, OpenData and OpenStandards are not as strong in chemoinformatics as they are in bioinformatcs, where it is common knowledge that sharing is a good. Today, the JCIM published on the web an article about the Blue Obelisk movement, which promotes these three idealogies.

You might have read earlier posts in this blog on CMLRSS, and received a question today on how to integrate CMLRSS with blogs on blogspot.com. Now, current CMLRSS feeds are normally generated with customized scripts, often directly from a database.

Gemma Holiday’s article on CMLReact was published in the january issue of the JCIM (doi:10.1021/ci0502698), which seems to be marked as sample issue right now. She used CMLReact as data format for MACiE (see doi:10.1093/bioinformatics/bti693), a database of 100 enzyme reactions, with fully annotated reaction mechanisms, making this an remarkable and insightfull database.

Roland Krause discussed today in his blog Notes from the Biomass an interesting website: postgenomic.com . This website, still marked BETA, mines blogs in the field of genomics and extract noteworthy statistics from it: which articles are cited in those blogs.

I was very pleased to read today that Kalzium, one of the projects that participate in the Blue Obelisk, got awarded! Cheers, Carsten!

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.

I never got around to mentioning this blog, but YAKAFOKON is a nice blog about, as the titel already says, bioinformatics, the semantic web and social networks. Nice to read, and interesting comments on the function and features of the internet and how they relate to bioinformatics, and science in general. Recommended!