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).
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 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.
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.
As promised , here is my list of submission for the Open Laboratory 2007:
Chemistry World December issue features a nice item on the future of data in chemistry: Surfing Web2O; Peter gave an excerpt , and Peter commented on it .
I recently saw that blogger.com blogs gained a poll feature. From now on, I will try to be a bit more Open Science, in addition to Open Source. From now on, you can be in my Advisory Board. To do so, vote on my next chemblaics (aka Open Source Chemoinformatics) project. The poll can be found on the left side of this blog.
My current jobs description is to speed up metabolomics data analysis, and finally got around to making a first relevant workflow for Taverna, using the webservices just posted over at ChemSpider: