chem-bla-ics: October 2006

Opensource Chemistry and Opensource Chemoinformatics

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. It seemed that this was contradicting, and Peter Murray-Rust [wp:en] wrote up a lengthy overview of the use of the term 'open'.

Oct

Running single JUnit tests in Eclipse

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'.

Oct

Being a good opensource user

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. A small patch excluded, I am really a regular user of these projects.

Oct

Are chemogenomics and proteochemometrics the same?

Joerg Wegner recently blogged about Chemogenomics: structuring the drug discovery process to gene families by C.J. Harris and A. P. Stevens in Drug Discov Today (DOI: 10.1016/j.drudis.2006.08.013). This review article provides a nice overview of a trend in mathematical modelling of the interaction of small organic molecules with proteins, often referred to as QSAR.

Oct

Google's new search engine: /* Code Search */

Google has set up a new search enginge specifically for source code: /* Code Search */. Important difference with their normal search engine is that it allows restricting your search by programming language, license and filename and package. I have not been able to figure out how to use 'package' yet, but the others are pretty clear. For example: AtomContainer license:LGPL lang:java should do it.

Oct

Bioinformatics: Open Source or Open Access??

I have heard that bioinformatics is ahead of chemoinformatics. However, I discoverd that this is not necessarily the case, while preparing for a homology modeling course I gave this week at the CUBIC. Open Access is really no issue there, with open access journals and many open access databases. But it is different when it comes down to open source software.