I have started using branches for non-trivial patches, like removing the HückelAromaticityDetector, in favor of the new CDKHückelAromaticityDetector . I am doing this in my personal remove-non-cdkatomtype-code branch, where I can quietly work on the patch until I am happy about it. I make sure to keep it synchronized with trunk with regular svn merge commands.

I have been working on a new atom type perception engine for the CDK, after having decided that the existing atom type lists where not sufficient for the algorithms we have in the CDK.

Ola has been doing a good job of integrating BioMoby support into Bioclipse. Earlier he completed a GUI for running BioMOBY services, and added more recently a JavaScript wrapper too, using the Rhino plugin developed by Johannes.

While Subversion is a signification improvement over CVS, they both require a central server. That is, they do not allow me to commit changes when I am not connected to that server. This is annoying when being on a long train ride, or somewhere else without internet connectivity. I can pile up all my changes, but that would yield one big ugly patch.

I just ran into BioSpider. Unlike ChemSpider, BioSpider crawls the internet (well, this list of sources really) to find information, and depending on what it finds it continues the search.

In this series I will introduce the technologies behind my FOAF network.

That must be a record!

A bit over two years I posted my first blog item, Chem-bla-ics , introducing the topic of my blog. In January this year I explained why I like blogging .

Bob has set up a new interface between the data model and the Jmol renderer, which allows him to define other types of export too. One of this is a POV-Ray export, which allows creating of high quality images for paper. Jmol has had POV-Ray export for a long time now, but never included the secondary structures or other more recent visual featues.

I added a Bioclipse plugin for JOELib (GPL, by Joerg) which comes with many QSAR descriptors, several of which are now available in the QSAR feature of Bioclipse :

The Open Data/ChemSpider debate is continuing, and Noel wondered in the ChemSpider Blog item on the Open Data spectra in ChemSpider. The spectra in ChemSpider come from four persons, two of which released their data as Open Data (Robert and Jean-Claude) and two as proprietary data.