Some time ago Rajarshi Guha introduced R bindings for the CDK (see his CDK News articles), and today I tried to install his rcdk package that makes it happen. However, it requires SJava which compiled fine on other machines, but not on my AMD64 machine. The problem seems to be related to the GNU GCC 4.0 compiler I have installed.

On the 7th International Conference on Chemical Structures Jeroen Kazius has a poster on finding discriminative substructures, that is, molecular fragments which can be discriminate between two acitivity classes. The software is released as Gaston, is written in C++ and has the GPL license. Later I encountered MoSS which has the same goal, but uses a different algorithm. MoSS is written in Java and uses the LGPL license.

Most Dutch chemists have their annual Lunteren meeting, so do I. Lunteren is a small village on the Veluwe where nothing much can be done, except for listening to the presentations. I participate in the Lunteren meeting for analytical chemists, i.e. HPLC, MS, GC and all their combinations upto and including HPLC/MS/MS, and since a few years the Lab-on-a-Chip stuff.

Just finished applying the latest spelling error fixes to CDK News 2.3 . Took me some three hours to finish it up the 12 pages, which has mostly to the need to recompile the PDF after each change to make sure that nothing in the layout got broken.

Jerome Pansanel contributed new patches for kfile_chemical; on Monday actually, but I have been busy with other things, among which a presentation I have to give next Monday for some 100+ analytical chemists. The patch adds support to KDE for five new chemical MIMEs: XYZ, Mol2, SMILES, VMD and GenBank. Therefore, I just released a new version (0.10), and added an announcement to Freshmeat.net.

Today is my 31st birthday, nearing half-point now (statistically seen). Also, by now I should have had my scientific moment of glory, otherwise I can forget that Nobel prize. Oh well, forget it. Have you seen those small advertisements on this page (RSS users, please visit the website :)? Funny links they give. The system is very nice btw: it awaits google indexing of the blog and then decides which ads are relevant.

Yesterday I had some spare time before going to a meeting about the Woordenboek Organische Chemie, so I was boldly going where no one has went before: getting the CDK module core independent of the data module.

A good functional molecular editor is of much important to the chemical web. There are a few small download sized editors around. JChemPaint has been available as applet for some time now, but the download size has been large. The situation has improved considerable over the past months, and the download size upon which the applet now shows up in your webbrowser is down to 538kB. A live demo is available from www.chemistry-development-kit.org.

Less then three months before the end of my contract of my PhD project. And not nearly done yet. Weekends are now spend on wrapping up bits of experimental research into something like a coherent article. And even lot’s of calculations to do to answer the open questions. FreeMind is helping me organize thoughts. Opensource chemoinformatics is a welcomed diversion now and then.

This week there was an interesting article in the Dutch Intermediar about viagra. They cite an article in Environmental Conversation and state that it saves the environment as it greatly reduced the market for animal parts from the traditional chinese medicine that address the same problem as viagra does. Viagra: good for the environment, good for you! ;) You don’t see this often, though.

CDK News 2.3 is scheduled for this month, and origanally planned to be distributed on the CDK5AW event. So, it’s a bit late. But the editorial process is converging… I realized that I forgot to mention the requirement for InChI’s whenever molecules are given.