chem-bla-ics

We all know chemical space; Chemical blogspace (Cb) is different: it is the chemistry discussed in blogspace. Cb is build on the opensource software of Postgenomic.com which I bloged on before. The now running Cb aggregates 19 blogs and, like the original, extracts linked (cited or reviewed) articles from literature.

The system is beta, but I am happy about it already that I mention it now. For example, some article titles are not properly recognized, and some journals are known in the statistics in several formats. And, more importantly, I have not yet hooked in the InChI support I developed earlier.

So, if you like the idea, or know other interesting scientifically interesting chemistry blogs, leave a comment, or send me email.

R News just released a special issue on the use of the versatile statistics program R in chemistry. It features six articles amongst which one by Rajarshi Guha on the CDK-R bridge, and one by my supervisor and me on the use of self-organizing maps to cluster crystal structures.

I hacked in a new extension point for Bioclipse yesterday, based on a proposal I made earlier. The new extension point (EP) is called ChildResourceCreator and allows creating child resources for a given IBioResource. One application where this is very useful is the CMLRSS application (earlier blog), or any RSS or Atom enriched with any other XML language. Here, child resources are created for each feed entry resource with as content the foreign XML, e.g. the CML bits in the blog.

Recently, a new generation of Chemical Markup Language CML users seem to hit the learning-curve-wall; there seems to be a niche in explaining the use of CML, so here goes. My new (third) blog will discuss frequently and less frequently asked questions about the use of CML.

Trepalin et al. published in Molecules the article A Java Chemical Structure Editor Supporting the Modular Chemical Descriptor Language (MCDL) (open access PDF). The applet is about 250kB (though the article mentions 200kB) in size and downloadable from the MCDL project on SourceForge (license: Public Domain). The article compares the applet with the JChemPaint applet and notes that their applet is much smaller.

Bling! Bling!. Mark Wielaard announced the GNU Classpath 0.92 release, with the following changes: an alternative awt peer implementation based on Escher that uses the X protocol directly. Various ImageIO providers for png, gif and bmp images. Support for reading and writing midi files and reading .au and .wav files have been added. Various tools and support classes have been added for jar, native2ascii, serialver, keytool, jarsigner. A GConf based util.peers backend has been added.

Mix one of the oldest and one of the latest computer technologies, and you get FoX (BSD license), a Fortran library for reading and writing Chemical Markup Language, and thus XML. Amazing, what Toby White achieved, though he did not start from scratch: "FoX evolved from the initial codebase of xmlf90, which was written largely by Alberto Garcia and Jon Wakelin." (source: cml-discuss mailing list).

Something I have not completely comfortable with about the CDK in the past, is the way Atom's are constructed:

IAtom carbon = new Atom("C");

Not that it is horrible code, but the CDK has an Element too.

Technorati is nice in several ways, one being the feature to set up a watchlist. I have set watches on chemoinformatics, Jmol, Bioclipse and a few more. This allows me see the latest blog items on these topics. Often, the point to Asian blogs, mostly Chinese and Japanese, which I mostly find hard to read.

Recently, a second beta of Java 6 was released, which triggered a patch for the Debian java-package package. It was a Bioclipse bug report today, however, which made me patch my java-package setup and install the beta.

So, next thing was to try to get the CDK compile with the Java 6 beta.