Well, you might spot a pattern here; yes, another chemical SPARQL end point (actually, it shares the end point with the Solubility data). This time around Rich’s ChemPedia.

With pleasure I read Analogue or Digital? - Both, Please. Funnily, I just created MP3 (or, preferably Ogg Vorbis, superior but hardly any support by commercial companies, who rather seem to pay license fees) directly from the CD.

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.

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.

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).

Johannes joined a Bioclipse Workshop a long time ago, and introduced the participants to the idea of using XMPP (aka Jabber) for asynchronous web services. SOAP is commonly user to run webservices over HTTP, but via (SMTP) email and XMPP is possible too (see SOAP over XMPP). Using HTTP as transport layer has problems. The biggest problem, is possibly that HTTP connections are timed out, e.g. by intermediate router.

There was some talk about the history of chemoinformatics toolkits by Noel and Andrew, which made me wonder on the exact history of Jmol and JChemPaint.

Cameron, Jean-Claude and I were invited to Peter’s place in Cambridge, where we are now hacking on CMLReact for the Ugi reactions Jean-Claude has been working on. I just finished a script that uses the CDK and Sam’s interface to the InChI library to convert a list of four reactants and one Ugi product into CMLReact (doi:10.1021/ci0502698). The full BeanShell script looks like:

Definately not a first post, but here are my experiences of my first blogging conference (see also this and this , the latter using semantic markup for the event): it was fun! My suggested unconference was not chosen, because I, as I usually do, focus to much on how instead of why one wants to do something. Nevertheless, I got to say my things, so I won’t complain.

I was doing some profiling (YourKit and Eclipse3.4) of the CDK atom typer, and it turns out that most time is spend on the perception of nitrogen atom types, which seems to be caused by the loadClassInternal() method of the JVM (java-1.5.0-sun-1.5.0.16 on Ubuntu Hardy):

Deepak asked me to comment on his blog post Is your web service open source?. With a slight delay, I did on FriendFeed. I’ll copy it here.