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.
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.
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.
My thesis was released slightly over a year ago in print form. The electronic form has not yet, which has social and legal barriers. Like many before me, I made the mistake to publish in journals that require me to reassign copyright.
FriendFeed is the missing link between social [bookmarking|news|…] and IRC (#cdk on irc.freenode.net); I quite like it. Anyway, as of today, they have a new layout, and that I do not like. No more icons for feed types, and big avatar photo’s. Really, I know what my fellow blogger look like (even met many of them in London last year). The rest of the layout is a bit too colourful for my taste.
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:
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.
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.
A long time ago (‘96 or so?), as a student with the no longer existing CAOS/CAMM (Google shows some traces, like this chapter describing the centre), I did a short internship with Hilbert Bruijn-Slot (I hope I remember his name correctly), where has asked me to look at data in the CSD, and in particular the prefered position of phosphate counter ions.
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).
This morning I finished setting up a RDF interface to the NMRShiftDB data (see nmr:234):