During my PhD I wrote a simple but effective genetic algorithm package for R. Because there was a bug recently found, and there is interest in extending the functionality, I have set up a SourceForge project called genalg. The package provides GA support for binary and real-value chromosomes (and integer chromosomes is something that will be added soon), and allows to use custom evaluation functions.

Third in the series of blogs about molecules in Wikipedia without an InChI (see also #1 and #2 ). There a certainly false positives, but here’s the updated list: http://www.en.wikipedia.org/wiki/AZD2171 http://www.en.wikipedia.org/wiki/Alizarin http://www.en.wikipedia.org/wiki/Allantoin http://www.en.wikipedia.org/wiki/Allylamine http://www.en.wikipedia.org/wiki/Alpha-ethyltryptamine http://www.en.wikipedia.org/wiki/Anthraquinone

Pedro reminded me of the last call for Open Laboratory 2007, which prints the best blog items of 2007 in book form. The list of chemistry contributions is not so large yet, so go ahead and nominate some of cool chemical blog items of the last year. I will post my shortlist later this week.

That’s why blogging works! I reported last Friday on using my Wii for reading Scintilla and Postgenomic.com. Alf replied: Ah, the trick word: TCP windows scaling.

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.