Profiling the CDK atom typer

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): less than 1 minute read

Scientific progress is a primary human need

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. 2 minute read

Mapping Peoples Interest: Google Insight Search

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): less than 1 minute read

"The End of Theory: The Data Deluge Makes the Scientific Method Obsolete"

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. 3 minute read

Online, multiplayer metabolomics game!

I was just organizing my toreads, when I found this link: metabolaspel.nl, an online, multiplayer metabolomics game! It’s in Dutch, but I guess anyone will get the idea :) Two teams, each may have two players, fight each other in sugar-fat conversion, by tuning the metabolism parameters: less than 1 minute read

CDK Literature #5

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. 2 minute read

Molecular QSAR descriptors in the CDK

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. This simplifies the QSAR descriptor calculation considerably, and, importantly, makes it more robust to the input. Though only by propagating errors into descriptor matrix. Just make sure your molecular structures have explicit hydrogens and 3D coordinates, and you’re fine. less than 1 minute read