Recently I discussed JUnit testing from within Eclipse , and blogged at several occasions about it in other situations. I cannot stress enough how useful unit testing is: it adds this extra set of eyeballs to make bugs shallow. And it does that, indeed. Ensuring that you actually test all the code you write, however, is not easy.

Just some short quites note about the third day (see day 1 and 2 ). Today’s program of the German Conference on Chemoinformatics started with a presentation by Rzepa about his work on a semantic wiki (DOI:10.1021/ci060139e), which might be online here. (He recorded a podcast, but I have not seen it online yet.) I wish I could see the sources of those wiki pages, to see how that system integrates RDF, but at least Jmol is running fine.

The 2nd German Conference on Chemoinformatics started yesterday, with two chemoinformatics tutorials: one on industrial chemoinformatics (I saw this presentation before… not sure when), with a good overview on integrating different information sources;

Paul Bracher and Joshua Finkelstein pointed my attention to a nice discussion in Nature on the future of chemistry, in What Chemists Want to Know, by Philip Ball. Paul and Joshua already reviewed it thoroughly, but I could not resist commenting in it too.

Open source chemoinformatics has become a common phenomenon, though many projects are small in nature: source code is developed by only few developers, or even in a closed manner and released when considered done.

The Bioclipse Workshop has ended and, for just three days, turned out quite productive. We have first bits of scripting support for JavaScript using Rhino. At this moment the scripting plugin needs to explicit depend on plugins to be able to access their classpath, but we plan to solve that. An example script: // to have short identifiers Array = Packages.java.lang.reflect.Array; String = Packages.java.lang.String;

Chemical Blogspace is up and running fine for some time now. Since the start the number of aggregated blogs increased from 19 to 64 now, of which a number are situated at ChemBlogs which is a site where you can run a blog. Meanwhile, the number of cited papers went up to 186! The JACS is most popular so far, followed by the Angewandte Chemie Int.

The Bioclipse Workshop is in progress, and Ola is now leading a discussion about future releases and functionality. Proceedings are live updated, and presentation sheets will be available shortly.

The Blue Obelisk mailing list has seen an interesting discussion on ambiguity in the term ‘open source’, triggered by a study by Beth Ritter Guth. For example, Jean-Claude Bradley performs ‘open source’ science (see his Useful Chemistry blog) who is not opposed to using closed source software, while the Blue Obelisk is about ‘open source’ software.

Unit testing is important when developing source code. JUnit provides a library to facilitate this in Java, and Eclipse had the functionality to run JUnit tests. Even better, it allows you to run single JUnit tests, even in debug mode: Just open the java class in your Package Explorer, right click on the JUnit method you want to run, then pick Run As or Debug As, and then JUnit test.

There are many ways to contribute to opensource software (OSS), programming only being one of them. I develop OSS, but use OSS too. For example, I am a big user of the Linux kernel, the KDE desktop, Kubuntu, Debian (I have unstable in a chroot), Firefox, Eclipse, Classpath, and many, many others. What these have in common, is that I generally have no time to look into the source code of these projects.