chem-bla-ics

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.

Half a year later we concluded that from the data which we started with (48 compounds with binding affinity), no conclusions could be drawn what so ever: no statistically sound models could be build at all. So, we composed three larger data sets. These sets, all QSPR data sets, did give us models, but all the spectra based models were worse than a Dragon descriptor based model using the same number of variables, without doing any variable selection.

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. I've spoken with twisti on the #classpath IRC channel, and he helped me run the compile with gdb, which indicated that at some point all threads were waiting.

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.

Starting last monday I'm at home, trying to get things finished as soon as possible.

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.

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.

Unfortunately, I had to reconfigure and restart my X11 each time my kids wanted to see Bob the Builder.