QSAR plugin for Bioclipse getting in shape

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. 1 minute read

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. 1 minute read

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: 1 minute read

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. 1 minute read

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. less than 1 minute read

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. 1 minute read

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. 3 minute read