Michael Koch (aka man-di) and Daniel Leidert (as part of the pkg-java team) have worked on packaging the CDK. The ran into some issues, such as the CDK build system not perfectly compatible with the Debian java libraries in /usr/share/java. Both detection of the available libraries as well as putting them in the classpath, caused trouble with the CDBS-based build system wrapping around the Ant build.xml (note the many commit this weekend ;).

Jim replied to the request by Anthony in my blog for a bug track system for CrystalEye (in beta), after a discussion on the CIF processing pipeline (see [here] (https://chem-bla-ics.linkedchemistry.info/2008/01/30/why-chemistry-rich-rss-feeds-matter.html), here, here and here).

Mathieu Fourment (et al.) just published a paper on some performance testing on 6 programming languages in BMC Bioinformatics: A comparison of common programming languages used in bioinformatics (doi:10.1186/1471-2105-9-82). The below figure is from the paper, for a sequence alignment exercise (copyright with paper authors, OpenAccess license of journal):

Today, Miguel (who made the 10000th CDK commit ) and I gave LaunchPad a go, because if offers a nice GUI for planning and monitoring source code development. We have set up a CDK team and a CDK project. LaunchPad has overlap with SourceForge functionality, but they idea is not to duplicate functionality. Moreover, we do not translate the CDK either, so that LaunchPad functionality is not useful either. Not for the CDK at least;

It has happened. Just a few minutes ago. The 10000th commit to the CDK source code repository. Miguel was the lucky(?) one.

Peter wrote up an item on Nick’s CrystalEye’s RSS feed, and I have been enthusiastic about chemistry-enriched RSS feeds for some time. CMLRSS has the chemical data inline in the RSS; see DOI:10.1021/ci034244p, the use of CMLRSS in Chemical blogspace described here and here , and the CMLRSS support in Bioclipse .

Wednesday is my regular day off from my metabolomics work, and today I am finalizing the layout of my thesis, which I’ll defend on April 2. The print version will feature grayscale images with some of them in color too. However, the PDF version that will end up in our university repository should have color prints. So, while halfway creating suitable grayscale versions of the image, I realized I was not doing it properly.

Setting up interactive web pages can be done in many way. Java Server Pages are just one of them. They are quite similar to PHP pages or Ruby , and combine plain HTML (and likely any other output) code with fragments of code; Java source code in this case.

No idea who the 22 persons are who were willing to join my advisory board , but they advised me to finish the JChemPaint work Niels worked on this summer :

Fourth in the CDK Literature series. Really, a follow up on #3 which I wanted to get out, even though not really finished yet. But, after 3 comes 4, not 3b. Maybe 3.1, but that suggests at least 3.2-3.9 too, let alone full R (that was supposed to the space of all reals…) I’ll stick to positive non-zero integers. #1 and #2 are still available too.

Third in a series summarizing literature citing one of the two CDK articles. See also #1 and #2 .