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

Nature Chemistry improves publishing chemistry: a detailed analysis

Nature Chemistry just released the first issue with a few free papers, like Asymmetric total syntheses of (+)- and (-)-versicolamide B and biosynthetic implications by Miller et al. (DOI:10.1038/nchem.110). 4 minute read

Editing and Validation of PubChem XML documents

With the general framework set up for editing and validation of CML documents , it was fairly easy to support the PubChem XML file format schema too. less than 1 minute read

Editing and Validation of CML documents in Bioclipse

One advantage of using XML is that one can rely on good support in libraries for functionality. When parsing XML, one does not have to take care of the syntax, and focus on the data and its semantics. This comes at the expense of verbosity, though, but having the ability to express semantics explicitly is a huge benefit for flexibility. 4 minute read

11 Years of Debian

11 years ago, a day more or less, I bought an the special issue of CHIP which shipped Debian 1.3.1. I think I’ve tried SuSe and RedHat earlier that year, but this Debian release made me switch away from proprietary products 98% (taxes I still had to do with Windows98). Right now, I am mostly running Ubuntu, which leans heavily on the work of the Debian project. less than 1 minute read