Chemical reactions in CML

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.

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Hot articles; mining the semantic web

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.

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Kalzium Wins Award; Carsten Niehaus Interviewed

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

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An test suite for free, open source JVMs

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.

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Tagging blog items

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. No idea, btw, how blog planets respond to them… For the record, the tags I list below are general for my blog, and not for this blog item specifically.

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A blog about bioinformatics, semantic web, comics and social networks.

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!

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Skype on Kubuntu using a Tiptel USB telephone

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.

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