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CDK Literature #4
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.
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CDK Literature #3
Third in a series summarizing literature citing one of the two CDK articles. See also #1 and #2.
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Open Lab 2007 results
The results for the Open Lab 2007 are out . I participated in this endeavor as judge, and read 75 of the 486 blog items, focusing on the sections chemistry, blogging, publishing, politics of science, and a number of blog items with few reviews when I passed them.
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Collaborative work with Bioclipse
Ola blogged about something he is working on for Bioclipse2. The next major series of Bioclipse releases will use the RCP-based resource architecture, which allows better integrating with other RCP plugins, such as the Subclipse plugin which allows one to browse Subversion repositories directly in Bioclipse. That is cool! Check out the screenshot he posted in his blog.
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Christmas presents...
Our Christmas tree has not been decorated yet, but the presents are there: the BMC Bioinformatics paper on userscripts in life sciences, Bioclipse 1.2.0, a long list of blogs to rate, and a very nice overview from Wendy Warr on workflow environments, discussing and comparing different offerings like Pipeline Pilot, Taverna, and KNIME.
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The molecular QSAR descriptors in the CDK
Pending the release of Bioclipse 1.2.0, Ola asked me to do some additional feature implementation for the QSAR feature, such as having the filenames as labels in the descriptor matrix. See also these earlier items:
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Test results for the CDK 1.0.x branch
The Chemistry Development Kit has never really been without any bugs, which is reflected in the number of failing JUnit tests. For trunk/ this is today 106 failing tests (live stats). The stable cdk-1.0.x/ branch, however, the number of failing tests is not much lower: 64 failing tests today (live stats).