CDK 1.2.7: the changes, the authors, and the reviewers

CDK 1.2.7 is the latest of bug fix releases in the 1.2 series. It brings a number of JavaDoc fixes, but, importantly, also bug fixes in SMILES handling and atom type perception. I am really pleased to see the application domain of various algorithms in the CDK continously grow: SMILES parsing for some transition metals has been fixed, and the SMILES generation for some types of ring closures too. Additionally, an important bug was fixed in the atom type perception algorithm, which failed for custom atom types with formal charges. Everyone using the CDK 1.2 series is advised to upgrade to this version. 1 minute read

Pulling out data as JSON from XHTML+RDFa

I am keen on RDFa and RDF in general; that should not be a surprise. RDFa is a serialization of RDF triples embedded in (X)HTML. I recently posted about chemical examples of XHTML+RDFa. Now, the reason for putting data in HTML as RDFa is that we can easily pull it out again, e.g. with this distiller. But the fun goes on, and we can actually also run SPARQL directly on it, for example with RDFaDev which I recently blogged about . 2 minute read

Second #acs_boston talk: teaching scientific communication

Below are the slides of my ACS CHED talk in Boston: less than 1 minute read

Handbook of Chemoinformatics Algorithms

As I was originally waiting for an actual copy inbox, which I still have not received, I had not blogged about it, but earlier this year the book “Handbook of Chemoinformatics Algorithms” by Jean-Loup Faulon and Andreas Bender got released for which I wrote a chapter on 3D molecular representation. Just wanted you to know. 1 minute read

Data duplication at Mendeley

Earlier this year I gave Mendeley a try, after having been a happy JabRef user, unhappy Connotea user (main problem was that any URI can be bookmarked, not just papers, so very noisy), happy CiteULike user (and still am). But the client did not bring me what I needed, and I canceled my account again. 2 minute read

BioMed Central is going to support Open Data

I had a glance at the plans already in the ACS in Boston , but this week BioMed Central announced a draft call for Open Data in their journals: 2 minute read

Added a Simile Timeline to my homepage

I finally got around to updating my homepage. Not entirely done yet, but it was overdue. The changelog includes a removal of the sidebar, which did not look nice when the page was embedded in my blog (the Home tab), foaf:interest RDFa annotation, a ToC line just below the header, and a Simile Timeline widget with my research positions and a selection of peer-reviewed papers: less than 1 minute read