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

Downloading Domoic Acid from PubChem

The identity of domoic acid has been under discussion (see here, here and here). (And I very much like the ChemSpider service to make it easy to copy data from ChemSpider into WikiPedia ChemBoxes; cheers!) less than 1 minute read

CDK 1.2.1 Released

I just released CDK 1.2.1 (aka The CDK Workshop 2009 Release), which is now available for download from SourceForge. The source can be found in our Git repository. The changes since 1.2.0 are mostly bug fixing, new unit tests, and minor clean up here and there: 2 minute read

Bioclipse2 Scripting #3: XLogP calculatation using a XMPP CDK cloud service

In preparation of the CDK workshop next week, here is a small Bioclipse2 script to calculate the XLogP value for a given SMILES, using the a CDK-based XMPP service: less than 1 minute read

Multiple inheritence for content types?

Bioclipse is an environment for handling and processing life sciences data. This data is present in files with a wide variety of formats, each of which can contain a particular data type. For example, a we can have a single molecule in MDL molfile and in CML. less than 1 minute read