Chiral Molecules: how cool is the SEM picture?

I just found my student thesis in Organic Chemistry from my Nijmegen education. It’s in Dutch, but I’ll explore if I can upload this to Radboud University’s DSpace. But I could not resist sharing this nice scanning electron microscope picture :) Look at those amphiphiles show a nice chiral ribbon! less than 1 minute read

ChEMBL 09 as RDF

Update 2021-02: this post is still the second-most read post in my blog. Welcome! Some updates: less than 1 minute read

Bioclipse-CDK-ChEMBL-SPARQL-Chemometrics mashup paper published

Our (peer-reviewed) Bioclipse-CDK-SPARQL-Chemometrics mashup paper was just published online (doi:10.1186/2041-1480-2-S1-S6) as part of the SWAT4LS 2009 supplement, where we use the CC-SA-BY-licensed ChEMBL database as example data source, based on a presentation I gave in Amsterdam back then. less than 1 minute read

Cleaner CDK Code #9: using the LoggingTool

A trick I used from Miguel Howard (of Jmol fame) is to not concatenate String until really needed. String concatenation will allocate new Strings, and thus burden the garbage collector (yeah, you lucky Fortran users who think twice before allocating memory :). Some time ago, he suggested this trick for the logger. I think in Jmol, but the CDK inherited that idea. 1 minute read

Adding a CDK atom type

A very quick, short post on CDK atom types. These atom types are used by the CDK to decide how many missing hydrogens an atom has, or how many lone pairs, and if the atom can be part of an aromatic ring system. The CDK code basically consists of three parts: the atom type ontology, the atom type perception code, and the rest of the code that uses information from the ontology. 2 minute read

CKAN and RDF: a nice example of why ontologies matter

For a while now I have been a so-called invited expert to the Linking Open Drug Data (LODD) task force of the W3C’s Health Care and Life Sciences Interest Group (HCLSIG). I also participate in the open-science group of the Open Knowledge Foundation (OKF). This is not really worth blogging about if the two are not being mashed up. Members from both sides are interested in learning how Open (think Is It Open Data?) the open data from the LODD network really is. 3 minute read

OPSIN used for a Bioclipse wizard

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