The Art of Programming: do not leak implementation details

At the JChemPaint workshop here in Uppsala, where we have Mark from Chris’ group as our guest, we encountered an inconsistency in CDK 1.2, where the bond stereochemistry did not yet follow the pattern recently adopted of having Class fields, to allow using null to have the semantics of undefined. Previously, the defaults for native values were confounded with set values. For example, the formal charge unset and 0 would be have a field value int = 0. 2 minute read

Updated Bioclipse SDK: the Eclipse 3.5 version

Last Friday, the Bioclipse 2.1 development series moved to Eclipse 3.5, so I had to update the Bioclipse SDK too, which we developed earlier . 1 minute read

NMRShiftDB RDF #2: Some statistics

This morning I had some more fun, and since the statistics view on the NMRShiftDB server is down, I though I could recalculate the statistics myself. Because the current RDF version of the data does not include all information yet, I cannot reproduce all of them. On the other hand, I can determine some other interesting statistics. 2 minute read

NMRShiftDB RDF #1: Spectra by InChI

Originally, I wanted to include a SPARQL query in my yesterdays blog showing how to retrieve NMRShiftDB spectra based on an InChIKey, but it horribly failed. I have yet to discover why. This morning I discovered that it is specific for that field, and that using the same thing with InChI is no problem: less than 1 minute read

NMRShiftDB enters rdf.openmolecules.net #2: SPARQL end point with Virtuoso

About 6 months ago I reported about my efforts to RDF-ize the data from the NMRShiftDB. Since then, time was consumed by many other things, but now that Bioclipse can query SPARQL end points, that I want to contribute the triple set (it is GNU FDL-licensed) to Bio2RDF, that a student started working in my group (now larger than just me :) on reasoning on life sciences data, and that I recently contributed my 1000th NMR spectrum to the database, I thought it was time to finally reinstall Virtuoso. 2 minute read

Open Knowledge: Reproducibility in Cheminformatics with ODOSOS

Below are the slides of my presentation of last Monday (see my earlier blogs ): less than 1 minute read

Google Wave robot for CDK functionality

I was really happy to hear early last week that I was invited to take part in the Google Wave beta, and received my account details this Monday, while at attending (and speaking at) the GDCh Wissenschaftsforum Chemie 2009. Yesterday was a travel day, and while working on course material for the Pharmaceutical Bioinformatics course that uses Bioclipse, I set up an Eclipse environment for development of a wave robot. Documentation was very clear, and deployment on Appspot one click on the appropriate button. Great work from the people from Google! It was all so easy, I could not resist pushing things a bit further, and looked carefully at other robots, like ChemSpidey by Cameron and Igor by Euan, to see how text replacement is done, and wrote my first functional robot, CDKitty (chemdevelkit@appspot.com): 1 minute read