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.
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.
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:
Free at last! Well, not quite yet, but close enough anyway: my PhD contract has ended; last friday was my last working day, which my collegues and I celebrated with a visit to Nijmegen oldest bar, In de Blauwe Hand . But I still have my manuscript to finish. This formally ends a period of almost 12.5 years at the Radboud University Nijmegen.
This is the best news I heard in weeks! The US Patent and Trade Offfice spoke with open source representatives about ways to deal with open source software as prior art. Apparently, their problem was how to be sure about release dates of open source, and authoritative sites like SourceForge.net, FreshMeat.net help a lot here, which extensive logging of releases.
While waiting for a Dragon calculation to finish (it does not work for molecules with more than 300 atoms!), I updated CDK’s build.xml to support gjdoc. The build script is now able to compile the custom doclets we use for creating the src/*.javafiles and others from the Java source files. And using gij I could also run CDK’s 1688 JUnit tests!
One of the things I had not fully figured out up to today, was how to configure my Kubuntu system to easily view DVDs on our TV, using my NVIDIA’s TV-OUT. I’ve seen xorg.conf files that define a X11 server for the monitor and a second for the TV, and files that use TwinView. Now, I did not really like the way first option worked, so tried the second.