chem-bla-ics

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. A couple of years back I read an article about Hansel, which does code coverage checking, but never got it nicely working for the CDK project. Never looked at that lately, so no idea how the current release would work out. Hansel is an extension of JUnit, and requires hard coding class names, which conflicts with CDK's module setup.

Thomas Kuhn pointed me last week to Emma, which seems a nice tool.

The 2nd German Conference on Chemoinformatics started yesterday, with two chemoinformatics tutorials: one on industrial chemoinformatics (I saw this presentation before...

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. Having chosen chemistry as specialization when I went to university, and with a minor in supramolecular chemistry, this is a something I do relate to.

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. Within open source software there is room for distinguishing a subset of open development chemoinformatics, that is, Bazar-like, instead of Cathedral-like (see ESR famous writing).

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. Ed.

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.