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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 anException, but returnsDouble.NaNinstead. The Exception is stored in theDescriptorValuefor 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. -
Commercial QSAR modeling? Sorry, already patented...
QSAR has been patented in 2001 (US patent 20010049585).
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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.
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Metabolomics needs you
Over on Metabolomics In Europe I posted a ad for an open metabolomics position in our group. Go check it out!
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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. -
Chemoinformatics p0wned by cheminformatics...
Noel had a 40 people vote over chemoinformatics versus cheminformatics. What do you think?
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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.