This autumn I will end my current post-doc position at Plant Research International in the Applied Bioinformatics group and at Biometris (both part of Wageningen University) funded by the Netherlands Metabolomics Center (lot’s of vacancies), where I had a good time, and collaborated in several projects within the NMC with much pleasure.

An open source project is as good as its community. Jmol has a brilliant community, but CDK is not doing bad either, in general at least; some CDK projects could use some more user feedback, such as CDK-Taverna (site down at the time of writing, but see the blog).

In addition to this Swing-based screenshot of JChemPaint , here’s a SWT widget in action (lower right corner):

Deepak informed me about Wordle via a FriendFeed notice, which can make nice visualisations of tag clouds.

Steffen reminded me over email that the particular machine only has a 1 dalton accuracy, and that the 150ppm parameter setting is somewhat inappropriate. As seen yesterday , it works fine for larger peaks, but fails for low intensity peaks.

One aspect not covered in detail by the ongoing discussion on unit testing quality control for scientific software, is detecting regressions. This is the most important reason why unit testing is superior to random testing. Putting someone behind a keyboard to tests things is nice, but this process has to be repeated, as the testing has to be repeated over and over again.

Define good. Let me say that up front. Good scientists, that is, if you say successful researchers are good scientists, secure good funding. Getting good funding requires doing the most relevant research (define relevant). Or, to put it bluntly, being a successful researcher requires to pimp your research. Doing boring research is nice for you, good for a Nobel prize if it turns out to have a cool spin off, but doesn’t buy you research success.

CDK QSAR descriptors are not allowed to change the input [molecule|atom|bond], and I recently added a unit tests (rev 11138) for that to the abstract class AtomicDescriptorTest.

CDK trunk is getting into shape, thanx to the many people who contribute to this, and special thanx to Miguel for cleaning up his code related to charge, resonance, and ionization potential calculations!

A quick screenshot, after some work on the JChemPaint code based on CDK trunk/. Nothing much to see, but a rather small code base, which is good. Today, I have set up cdk/cdk/trunk/ and cdk/jchempaint/trunk as Eclipse plugins, allowing the second to depend on the first. So, no more use of svn:externals.

Following many, many others, I finally got myself a SlideShare account and uploaded a recent presentation on MetWare, our metabolomics data warehouse project. Some spoilers: SQL, RDF/SKOS, JSF.