On my desktop, the Scintilla and Postgenomic.com websites do not work. It is not a browser problem, but has something to do with TCP/IP packages not reaching its destination: the browser. Euan told me they are aware of the problem, but apparently have not found a solution yet.

Right at this moment I am listening to Andrew Hopkins from Dundee on chemical opportunities in system biology, at the Cytoscape conference in Amsterdam . Anyone who wants to meet up over lunch or coffee break?

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. For example: console = Packages.net.bioclipse.util.BioclipseConsole; moby = Packages.net.bioclipse.biomoby.ui.scripts.MobyServiceScripting; biojava = Packages.net.bioclipse.biojava.scripts.BioJavaScripting;

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. Below is a screenshot of an intermediate point after starting with the InChI of methane: After the search it generates a long HTML page with all the information it found on the molecule you queried for.

In this series I will introduce the technologies behind my FOAF network. FOAF means Friend-of-a-Friend and My FOAF file (draft) will give you details on who I am, who I collaborate with (and other types of friends), which conferences I am attending, what I published etc. That is, I’ll try to keep it updated. BTW, FOAF is a RDF language.

That must be a record! Eric Jain wrote on public-semweb-lifesci: I surely hope this is not the last we hear of this huge RDF collection.

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 : Meanwhile, the Bioclipse team in Uppsala has set up the obligatory scatter plot functionality, but leave that screenshot for them to show. Therefore, time for integration with R.