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 .
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.
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.
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.
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.
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).