Chemical blogspace has seen a lengthy discussion on the quality of a few NMR shift prediction programs, and Ryan wanted to make a final statement. Down his blog item he had this quote from Jeff, discussing the use of the NMRShiftDB as external test set: I’m sure none of us knows what weird chemistry people are doing;
Everyone of use knows that big pile of paper on your desk that contains the things we want to read, scan or just browse. I even have an electronic equivalent. Another pile contains leaflets and glossy folders from conferences, like the ACS meeting in Chicago. OK, going to get rid of those last ones, and will shortly put the links here. The first leaflet is from Chemistry Central, one of the open access publishers.
The Seven stones wondered what to do with a petaflop in science, in response to Declan’s The petaflop challenge in Nature.
Atom typing is one of principal activities in chemoinformatics. Atom types provide additional information that cannot be derived from the connection table that is being used, or may define what force fields terms should be used. This makes perception of atom types very important. The CDK has a few places where atom types are perceived. The HydrogenAdder and ValencyChecker are two examples.
December last year I proposed the use of microformats and RDFa for simple semantic markup of molecular information.
Over the last few weeks I continued the work on getting (descriptor-based) QSAR/QSPR implemented in Bioclipse. JOELib (GPL) and the CDK (LGPL) being two prominent opensource engines that can calculate molecular descriptors, and AMBIT a front-end. To be able to do QSAR/QSPR model building from start to end in Bioclipse, I worked in April on an architecture for selecting descriptors.
Pedro suggested in Nature Networks What’s Next forum that Nature should add a new service for scientists: hosting electronic lab notebooks. And I think this will be a killer application. I am rather excited about the idea, and feel ashamed not putting one-and-one together myself.
Last week I started the Blue Obelisk Chemical Test File Repository, a repository of OSI-approved-licenced test files (from various sources) to improve interoperability between chemoinformatics software. Following a discussion on the mailing list earlier, a directory hierarchy has been set up, and each files contains an index.xml to describe the content.
Ryan blogged in Archive This about some advices from ACD on how to store spectra in your electronic lab notebook. Use InChI This reminded me of a discussion I had with with Colin when he was at the CUBIC, which was about experimental sections. I proposed that the InChI should have a prominent place in the experimental section.
On July 1st I will start a post-doc in Wageningen, The Netherlands at the WUR. More precisely, with a post-doc in the group of Prof. Van Eeuwijk at Biometris, cooperating with the group of Prof. Hall at Plant Research International (PRI), within the framework of the new Netherlands Metabolomics Center.
Lately, Chemical blogspace has seen an interesting discussion on the quality of opendata and free chemical database (over 32 free resources now ), such as the NMRShiftDB.org. For example, see Antony’s view on the NMRShiftDB and Robien’s analysis. Opendata makes such quality assurance possible, and I am happy that the NMRShiftDB was explored like this; the found problems can be reported and corrected.