chem-bla-ics: July 2008

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.

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. The CDK has been used to create SMILES.

Roman Klinger, Corinna Kolárik, Juliane Fluck, Martin Hofmann-Apitius, Christoph M.

Jul

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.

Jul

Commercial QSAR modeling? Sorry, already patented...

QSAR has been patented in 2001 (US patent 20010049585).

Jul

Peer reviewed Chemoinformatics: Why OpenSource Chemoinformatics should be the default

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.

The battle for chemoinformatics, however, has not even started yet. The Blue Obelisk paper (doi:10.1021/ci050400b) has gotten a lot of attention, and citations. But closed source chemoinformatics is doing fine, and have not really openly taken a standpoint against open source chemoinformatics.

Jul

Metabolomics needs you

Over on Metabolomics In Europe I posted a ad for an open metabolomics position in our group.

Jul

Going to Science Blogging 2008: London

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.

Jul

Chemoinformatics p0wned by cheminformatics...

Noel had a 40 people vote over chemoinformatics versus cheminformatics. What do you think?

I have thrown in two extra options: chemblaics (from my blog: chemblaics (pronounced chem-bla-ics) is the science that uses computers to address and possibly solve problems in the area of chemistry, biochemistry and related fields.

Jul

SVN commit hooks down for CDK and Bioclipse

SourceForge has been playing with system upgrades again, and in an attempt to debug the failing CIA commits on IRC, I reinstalled the hooks for CDK and Bioclipse, so that now all hooks seem to fail, including the email hook... Apparently, it is a known bug, e.g. see this bug report. I assume SF will fix this soon.

On the bright side, I also noted an updated webpage for SF uptime/problem tracker, where it is also reported that stats are currently down for upgrade.

Jul

Moving to Sweden: Improving CDK support in Bioclipse

This autumn I will end my current post-doc position at Plant Research International in the Applied Bioinformatics group and at Biometris (both part of Wageningen University) funded by the Netherlands Metabolomics Center (lot's of vacancies), where I had a good time, and collaborated in several projects within the NMC with much pleasure.