Doesn’t happen often, but my machine crashed two hours ago. Not a big deal, because I have my important files in SVN. Oh wait, SVN had a commit in progress during the crash. So, svn recover. Mmmm… doesn’t work either. OK, SVN FAQ: try db_recover. That worked. No, it did not: svn commit still not working for the files I was trying to commit.
Some weeks back there was the CDK5AW , the CDK 5th anniversiry workshop. A small group of international open source chemo-, bioinformatics software developers met, among which two from Sweden. It was then decided to generalize their work resulting in Bioclipse: https://www.bioclipse.net/ It’s heavily using the Eclipse Rich Client Platform , making additional plugins trivial.
Thanx to Mark’s encouragements, I tried to run Jmol and JChemPaint with jamvm. Jmol fails with an NullPointerException , but JChemPaint runs! And note that this was not even running with the latest of the latest; just recent packages from Kubuntu! Yes, there are some glitches, but I’m happy nevertheless!
This evening I have been looking at with the KNOPPIX customization howto, and ran many of the interesting commands. I’ve setup a environment with Kalzium, OpenBabel, CDK, jython, PyMOL, and for development I included gcj and Eclipse. At some later point I will include kfile_chemical too, but I want to make a deb package first.
OK, just back from the first German Chemoinformatics Conference, which I enjoyed very much. A rather interesting program, and lots of interesting posters too. You can read the programme online, and will not spend too many words on that (at least not now). But what I will do is point out some interesting posters here. One poster was on the Molecular Query Language (MQL) by Ewgenij Proschak from Frankfurt.
This sunday starts the first German Chemoinformatics Conference in Goslar. It’s an interesting programme , with presentations on the InChI, PubChem, 25 years of chemoinformatics, the chemical semantic web, and much more. Among these presentations is mine, on comparing crystal structures (PDF ) and deducing cell parameters. But I’m having a poster on QSAR too.
Not so long ago, it was decided that KDE 4.0 will use SCons as a configuration and building tool, instead of the autotools and make: the common ./configure && make && make install which has served the open source community very well for so long. SCons is different in several ways.
Yesterday I reviewed an article which published a QSPR model which looked something like: \[y = 151 + 50p1 - 12p2 - 0.006p3\] with quite OK prediction results (R=0.9880). But I was not quite comfortable with the coefficient for the \(p3\) variable. The article did not calculate significances for the coefficients, so it was not obvious from the article wether is was useful to include them. I then looked at the range for p3, which was 110-150;
The great thing about open source is that… it’s open. When I was browsing the internet just now, I dropped in on KDE Dot News. In the rightside column, there is a feed of new KDE software from KDE-apps.org. A new version of my favoriate music player, amarok, lured me to the KDE-apps website, where I saw rkward is latest announcement.
I just read that the Kubuntu team wants to include Kat in the dapper release (scheduled for April 2006). Kat is (to be) the KDE equivalent of Google’s desktop search bar. This is great news for us chem-bla-icians, as Kat has support for full text searching of chemistry files! Let’s see if I can get the Kubuntu team to package up kfile_chemical too, which will extend Kat (and KDE in general), with extraction of meta data from chemical documents.
On the 7th International Conference on Chemical Structures Jeroen Kazius has a poster on finding discriminative substructures, that is, molecular fragments which can be discriminate between two acitivity classes. The software is released as Gaston, is written in C++ and has the GPL license. Later I encountered MoSS which has the same goal, but uses a different algorithm. MoSS is written in Java and uses the LGPL license.