ChemPedia RDF #1: the SPARQL end point

Well, you might spot a pattern here; yes, another chemical SPARQL end point (actually, it shares the end point with the Solubility data). This time around Rich’s ChemPedia. Taking advantage of the CC0-licensed downloads , I have created a small Groovy script (using this JSON library) to convert the ChemPedia JSON into Notation3: 1 minute read

CDK 1.2.4: the authors

The CDK 1.2.4 changelog I posted earlier was directly created from git output. Git has many features which makes such thing simple. Here’s a list of authors of the 1.2.4 change set: less than 1 minute read

CDK 1.2.4: the changes

Here is the changelog of CDK 1.2.4 which I am about to upload to SourceForge: 6 minute read

BlueObelisk StackExchange (.com)

Oh no, not another communication channel?! We already have Google Wave! (BTW, I have quite some new invites…) less than 1 minute read

Call for Collaboration: JavaDoc validation with OpenJavaDocCheck

I reported recently about my efforts to write an Open Source DocCheck replacement. I received the first patches (from Rajarshi), and brought it online in a CDK branch (see this Nightly page). 1 minute read

New Bioclipse Features: Kabsch Alignment, RMSD Distance and Tanimoto Simarlity Matrices

We recently submitted a second paper on Bioclipse, and have worked hard in the past two weeks on addressing the reviewers’ questions (and we love these feature requests! See also these two blogs). One reviewer seemed very interested in seeing docking available in Bioclipse. While we do not have a full docking feature set up for Bioclipse, we do have functionality to deal with 3D structures, though our researched urged us to focus on the 2D side of cheminformatics so far. 3 minute read

Milestones...

While I am still looking around for a assisting/associate professor position, there are two milestones around my scientific work I want to briefly mention here. This blog is the 500th blog on chem-bla-ics, and the two CDK papers have combined reached 100+ citations as counted by Web-of-Science, as can be seen on my ResearcherID profile. less than 1 minute read