Some days have passed, and the Debian mirrors have now picked up the CDK package (unstable only so far), allowing you to sudo aptitude install libcdk-java from your favorite local mirror. The details are available from this packages.debian.org/libcdk-java page. The fact that it is listed as contrib is a small mistake; the package is really main material.
Michael Koch (aka man-di) and Daniel Leidert (as part of the pkg-java team) have worked on packaging the CDK.
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, here, here and here). Instead of setting up a BTS at SourceForge, locally with Bugzilla, or at LaunchPad, he suggested to use Connotea: Now, Connotea is advertised as a [f]ree online reference management for all researchers, clinicians and scientists , and I have never really
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): Nothing shocking, I’d say;
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. From our IRC channel #cdk on the irc.freenode.net network: [19:55] cdk: miguelrojasch * r10000 /branches/miguelrojasch/ reaction/src/org/openscience/cdk/ (2 files in 2 dirs): Removed Flags. They were not used anymore.
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. Ubuntu’s tomcat5.5 package installs quite easily, and sets up a server at port 8180. I still have to figure out how to nicely integrate it with the Apache server on port 80, though.
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: Like my current main hobby project (atom typing in the CDK), the JChemPaint project will be performed in my non-working hours mostly. A reasonable ETA is, therefore, end of this summer. Main discussion on will be done on the cdk-jchempaint mailing list.
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.