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.
As promised , here is my list of submission for the Open Laboratory 2007: Open Data is critical for Reproducible Research If you ever made something fluoresce after you did a reaction with a transition metal… One For the Brave Fun with singlet oxygen SMILES and Aromaticity: Broken?
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 . The article discusses many of the things that have been happening in the field of chemical data. It touches Jean-Claude’s work on Open Notebook Science, and then moves to Peter’s Open Data, mentions a number of other blogs and the Chemical blogspace.
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: I uploaded the source to MyExperiment, so anyway can play with it. There is much to improve, such as using CDK-Taverna for further analysis of the results.
The Applied Bioinformatics at PRI group where I now work in Wageningen and the group of Steffen Neumann in Halle have started the MetWare project on Sourceforge to develop opensource databases for metabolomics data.
