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.
Noel had a 40 people vote over chemoinformatics versus cheminformatics. What do you think?
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.
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.
An open source project is as good as its community. Jmol has a brilliant community, but CDK is not doing bad either, in general at least; some CDK projects could use some more user feedback, such as CDK-Taverna (site down at the time of writing, but see the blog).
In addition to this Swing-based screenshot of JChemPaint , here’s a SWT widget in action (lower right corner):