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.

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. Several open source projects participate, amongst which the CDK, Jmol, JOELib, OpenBabel, Chemical Markup Language, Bioclipse and Kalzium.

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. So, here’s my attempt to include CML in a blogspot.com blog. OpenBabel 2.0 can create good CML, for example for acetic acid: Nothing much to see, right?

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. For example, the most discussed article is Kai Wang’s Gene-function wiki would let biologists pool worldwide resources in Nature.

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!

If you have read my previous post and visited that other blog, you might have noted the Technorati keywords . Or tags, really, as explained in this rel=”tag” microformat. Adding them to blog items, will enable indexing by Technorati, one of the bigger blog search engines. So, from now on, you’ll see these tags in my items too, hoping they don’t get annoying.

Because I wanted to test internet telephony I downloaded Skype and tried to get it to work on my Kubuntu system. Unfortunately, the Skype version is only 1.2.0.18, and it does not work well with arts :( That is, using artsdsp it crashes with segfaults whenever I start even a chat, let alone a phone call. This could be worked around by disabling sound in my KDE session, and then the /dev/dsp is open again.