Critical mass for Open Notebook Science wikis by prepopulation with RDF data

One of the problems with Open Data, - Source, and Standards (ODOSOS) is to get critical mass: for the project to move forward, you need both a good user community and an active developers community. The first is the crucial reward for the latter: people using your work is the incentive. Sometimes, a project does not succeed in doing that; Rich was questioning if his ChemPedia project built up enough mass. 2 minute read

All CrystalEye data available as PDDL

I do not think I have seen this earlier, but I do not visit the homepage regularly. But congratulations to the CrystalEye team for releasing the data explicitly as PDDL! I cannot stress enough how useful it is if you add a statement like this to your public domain data. Well done! less than 1 minute read

Looking at your statistical models...

I do not think I have ever blogged the paper that played an important role in my thesis (doi:10.1021/ci990038z); research of one of the papers in my thesis, started with the hypothesis proposed therein. The paper had a really good idea; but, unfortunately, it did not contain the data to support the hypothesis. That gets me to one important lesson I learned: a QSAR data set of less than 100 molecules is not enough to make untargeted statistical models. 4 minute read

QSPR modeling with signatures

I had to dig deep to find posts on QSAR modeling. There are quite a few on QSAR in Bioclipse, but that focuses on the descriptor calculation. In a quick scan, I could only spot two modeling posts: 3 minute read

My OpenTox Workshop contribution: The Lost Slides

During the nice presentations at the recent OpenTox Workshop, I noted that My OpenTox Workshop contribution: Linking explicit and implicit knowledge was lacking two slides. The slides should have had screenshot of the excellent Bioclipse applications Ola Spjuth has written in the area of computational toxicology. But here they are. 1 minute read

I’m just a sucker with no self esteem

Don’t let anyone fool you: The Offspring is really just talking about Science: less than 1 minute read

CDK-JChemPaint #6: rendering atom numbers

I have made a few new CDK-JChemPaint patches in the past two days, the latest being patch 15. With the help from Gilleain, all rendering parameters are now using the new API, as explained earlier in this series. 2 minute read