chem-bla-ics: March 2009

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.

BTW, Helena's thesis is partly Open (see Peter's “should theses be Open?”). Partly, because it has the thesis parts which have not been published in journals before.

Mar

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.

Mar

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.

Mar

Preferential positions of phophate counter ions

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.

Mar

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).

Now, we've seen the Royal Society of Chemistry's Project Prospect (see RSC: the first publisher to go semantic!) and ChemSpiders recent ChemMantis system which enriches the papers with machine readable representations of the molecules discussed in those papers.

Mar

NMRShiftDB enters rdf.openmolecules.net

This morning I finished setting up a RDF interface to the NMRShiftDB data (see nmr:234):

And made links between the new frontend and rdf.openmolecules.net, make the Linked Open Chemistry Data (LOCD) network grow (naming following Linked Open Drug Data). In comparison with the previous depiction, I added arrows to indicate the direction of the linking.

Mar

Autogenerating CML bindings for XMPP services with XMLBeans

I blogged earlier about our efforts to create a better SOAP service architecture, based on XMPP:Details behind the "Calling XMPP cloud services from Taverna2"Calling XMPP cloud services from Taverna2Next generation asynchronous webservices So, I set up XMPP services for QSAR descriptor calculation, 2D diagram and 3D geometry calculations and a few more, using the CDK.

Mar

Bioclipse: a powerful Jmol application

While Bioclipse is much more, it could be an interesting alternative to the Jmol application.

Mar

Open NMR data: raw curves and annotated peak lists

Games are known to trigger technical innovation. But recently it also triggered innovation on open chemical databases. Jean-Claude reported:We are very excited by what we have put together so far. There are currently 457 H NMR, 389 C NMR, 11 IR and 29 NIR spectra.

Mar

Open Data versus Capatalism?

Ian Davis was recently quoted saying open data is more important than open source, which was pulled (out of context) from this presentation. The context was (a slide earlier): Data outlasts code.

As far as I can see, this is utter nonsense, even within context of the slide (see also this discussion on FriendFeed). Obviously, within the context of Ian it does makes sense, and I hope he will respond in his blog and explain why he thinks Open Data is more special.