I was doing some profiling (YourKit and Eclipse3.4) of the CDK atom typer, and it turns out that most time is spend on the perception of nitrogen atom types, which seems to be caused by the loadClassInternal() method of the JVM (java-1.5.0-sun-1.5.0.16 on Ubuntu Hardy):
Google has a new service: Google Insight Search, and I was wondering if it could tell me to use chemoinformatics or cheminformatics… No, it can’t. In both there is a declining interest (only chemoinformatics shown):
Deepak asked me to comment on his blog post Is your web service open source?. With a slight delay, I did on FriendFeed. I’ll copy it here.
The thought triggering editorial “The End of Theory: The Data Deluge Makes the Scientific Method Obsolete” by Chris Anderson can’t have escaped your attention. I was shocked when I read the title and the comments made on the blogosphere and on FriendFeed.
I was just organizing my toreads, when I found this link: metabolaspel.nl, an online, multiplayer metabolomics game!
Time flies. Another CDK Literature (see also #1 , #2 , #3 , #4 ). Quite a few papers have been published again, and I’ll briefly discuss a few of them. Detection of IUPAC names Klinger et al. have written a paper on detection of IUPAC names. As long as semantic markup languages are not the default, this remains important. Remaining problems include correctly finding boundaries in summaries of chemical.
Rajarshi has patched trunk last night with his work to address a few practical issues in the molecular descriptor module of the CDK (and I peer reviewed this work yesterday ). One major change is that the IMolecularDescriptor calculate() method no longer throws an Exception, but returns Double.NaN instead. The Exception is stored in the DescriptorValue for convenience.
QSAR has been patented in 2001 (US patent 20010049585).
The battle for scientific publishing is continuing: openaccess, peer reviewing, how much does it cost, who should pay it, is the data in papers copyrighted, etc, etc.
Over on Metabolomics In Europe I posted a ad for an open metabolomics position in our group. Go check it out!
On Saturday 30th of August I'll be in London attending the Science Blogging 2008 event. The Monday following that, I'll meet friends at the EBI, but Sunday is empty so far. I'd love to meet up that Sunday, so just ping me if interested. Oh, and this blog is using RDFa to markup the event, as discussed here.