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.

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Quality of Chemical Database

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.

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Using Wikipedia to recognize Molecules in Blogspace

Only few people are using InChI’s to indicate the molecules the blog about (prominent exceptions are Useful Chemistry and Molecule of the Day). Consequently, the number of detected molecules (without using OSCAR3) in Chemical blogspace has been low.

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Payed summer jobs in chemoinformatics

Last year the Programmeerzomer.nl sponsored one summer student to work on Bioclipse (see the announcement). The Programmeerzomer is much like the Google Summer of Code where I mentor Alexandr. However, it is much smaller and oriented at just the NL area: both the student and the mentor needs to be Dutch, but the opensource project does not.

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Janocchio: Jmol and CDK based 1H coupling constant prediction

While looking up a reference for FirstGlance in Jmol, I found Janocchio, a CDK and Jmol based tool for prediction of coupling constants, recently published in Magnetic Resonance in Chemistry. It’s written by Evans, Bodkin, Baker and Sharman (from Eli Lilly) and licensed LGPL. It is one of those rare contributions of pharmaceutical industry, and I can only deeply appreciate this contribution.

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Preprint servers: the CPS failed, how will Nature Precedings do?

Some 7 years ago, following successes in physics, ChemWeb.com launched the Chemistry Preprint Server (CPS), and Warr evaluated it in a JCIM article three years later. She wrote about ‘lessons learned’, but the only one seemed to have been that chemistry was not ready for it, as the project shutdown in 2004. The archives are still available, fortunately, and you may find it amusing to look up my or some other submission.

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Scientific Literature: searching, ranking, storage

Dealing with scientific literature has been one important theme in Chemical blogspace. For example, ranking articles and how to store your personal PDF archive has been topics of discussion. In this blog I will summarize bits of the discussion, and my personal view on things.

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