Bioclipse and SPARQL end points #2: MyExperiment

RDF and SPARQL are two really useful Open Standards. Bioclipse-RDF is a plugin for Bioclipse that provide RDF functionality, among which using remote SPARQL end points. 3 minute read

Bioclipse and SPARQL end points

Last week, there was a very interesting thread on the DBPedia mailing list, on using Java for doing remote SPARQL queries. This was one of the features still missing in bioclipse.rdf. Richard Cyganiak replied pointing the code in Jena which conveniently does this and which bioclipse.rdf is already using anyway. Next, Fred Durao even gave a full code example relieving me from any further research, resulting in sparqlRemote() now implemented in the rdf manager: less than 1 minute read

Bioclipse-JChemPaint

The Uppsala and EBI CDK-teams have been working hard on finishing the rewrite of JChemPaint I started with Niels earlier. While the EBI-team focused on the applet (and Swing application), the Uppsala team, obviously, focused on the SWT side, for integration into Bioclipse. The new JChemPaint is reaching a useful state, and below is a quick update screenshot something Arvid has been working on: less than 1 minute read

CDK - The Documentation

In preparation for the CDK workshop later this month, I am writing up my material for my kick-off presentation of the workshop. So, I better make it good. Using LaTeX at least overcomes my laziness which always made Word documents look stupid. Even default LaTeX looks good: 1 minute read

StARlite talks in Uppsala; Helena's Open Chemogenomics thesis

John was in Uppsala last Friday, and our group had the pleasure of talking to/with him before he was opponent to Helena defending her thesis on Chemogenomics: Models of Protein-Ligand Interaction Space (ISBN:978-91-554-7430-0). Since we believe we can do tons of really interesting science on John’s StARlite data, I was excited to talk to him in person. He gave three talks that day, and managed to keep the overlap minimal (yes, not quite an absolute measure, but you get the point). We showed him the efforts of Arvid, Carl, Jonathan and me on converting the StARlite data to RDF, on which I will write shortly. 1 minute read

Highlighting Console output in Eclipse with Grep Console

I ran into an Eclipse Grep Console plugin (EPL license) today that takes regular expression to color output in the Console. Given the amount of output Bioclipse and the CDK give when in DEBUG mode, this allows me to highlight those bits I am interested in. For example, comments on the Bioclipse managers: less than 1 minute read

Journal of Cheminformatics: I hope the Instructions to the Authors improve

Besides Nature Chemistry , another journal was launched last week (see here and here): the Journal of Cheminformatics. First of all, congratulations to Chris and David for their efforts! While the journal only published one research paper yet, it already found its place on Chemical blogspace. I have two things I want to blog about: data rich publishing, and starting the scientific communication. 4 minute read