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. Reviews Two reviews have recently appeared which cite the CDK. Ricard Stefani has written a review in Portuguese of the many NMR-based elucidation tools on computer-aided structure elucidation. The CDK is cited as a general chemoinformatics tool. It also cites SENECA which uses CDK’s structure generators.

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. Now, this kind of integration is important.

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. I am happy to see that one of the chemistry submission I made myself made it into the anthology: the Depth-First item on SMILES and Aromaticity: Broken?

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.

The OD part of ODOSOS is getting more and more attention, and it seems that Peter’s Open Data battle is paying off (see his original OpenData article in Wikipedia): an open data specific license has reached the beta stage (see this announcement). The idea behind this licenses seems to come down to: I am looking forward how this license will be picked up by the community. PubChem may be a good candidate to use this license;

The comment I left in the ChemSpider blog, was probably a bit blunt. ChemSpider announced having licensed software from OpenEye. I have seen such announcements more often, but am intrigued about the nature of such announcements. Is it bad that ChemSpider is using OpenEye software? Certainly not.

Controlled vocabularies, hierarchies, microformats, RDF. Nico Adams pointed me to this excellent video: It’s a really nifty piece of work, which goes into the differences between thesauri, controlled vocabularies, and, as such, ontologies, and social tagging systems. Both have their virtues; it is fuzzy logic versus ODEs all over again. Whether one is better than the other only depends on the problem at hand.

I was pleased to hear that Christoph will move to the EBI early next year. Christoph has been working on Open Source and Open Data chemoinformatics since at least 1997. I first got in contact with Christoph when I wrote code for JChemPaint (which Christoph developed) to be able to read Chemical Markup Languages (CML). This also got me into contact with Dan Gezelter who is the original author of Jmol, to which I also added CML support.