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Atom typing in the CDK
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.
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Chemical RDFa with Operator in the Firefox toolbar
December last year I proposed the use of microformats and RDFa for simple semantic markup of molecular information. I linked that with the InChI extension for the Postgenomic.com software for Chemical blogspace and wrote these tools to work with the markup:
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Test File Repository and RelaxNG
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.
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Nature should host our Electronic Lab Notebooks
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. We have our chemoinformatics tools and RDF is just around the corner, that combined with semantic wikis, and we have science of the 21st century. This is my reply posted on Nature Network:
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Archiving spectra: use InChI and CML
Ryan blogged in Archive This about some advices from ACD on how to store spectra in your electronic lab notebook.
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A new job: post-doc at the WUR on MS based structure elucidation
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. The topic will be structure elucidation using mass spectral data originating from the experimental department of PRI, and will be a nice follow up on the work on SENECA I have been doing last year in the group of Dr. Christoph Steinbeck at the CUBIC.