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!
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.
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.
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.
Recently, a Dutch version of Google News was started, and might mean a replacement for nu.nl. I do not like the verbose layout much, because it makes it more difficult to scan headlines. I do like the themes. Except for one. The English theme ‘Sci/Tech’ is Wetenschap in the Dutch version, or plain Science. And it annoys me to read IT headlines when looking up scientific news.
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.
About two years ago a student started with me to work on the use of 1D NMR and IR spectra in quantitative structure-activity relationship (QSAR) work, with the goal to show that these spectra contain 3D information relevent to QSAR models. It is known that these spectra depend on the 3D conformation of the molecule.
Because I am still looking forward to testing CDK against the latest Classpath 0.20, I downloaded cacao 0.94-1 for Debian sid, then tried to compile CDK with it: JAVA_HOME=/usr/lib/jvm/cacao ant -Dbuild.compiler=gcj clean test-all But that hangs at some point with zero load. I have no idea what is going on there.