Chemical Blogspace updates

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.

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Bioclipse Workshop: short but productive

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:

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The Bioclipse Workshop is in progress

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.

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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’.

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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:

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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.

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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. What the article does not discuss, is the work by the group of Jarl Wikberg who coined the term proteochemometrics (see PubMed: 11342268).

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