Lately, Chemical blogspace has seen an interesting discussion on the quality of opendata and free chemical database (over 32 free resources now ), such as the NMRShiftDB.org. For example, see Antony’s view on the NMRShiftDB and Robien’s analysis. Opendata makes such quality assurance possible, and I am happy that the NMRShiftDB was explored like this; the found problems can be reported and corrected.

Only few people are using InChI’s to indicate the molecules the blog about (prominent exceptions are Useful Chemistry and Molecule of the Day). Consequently, the number of detected molecules (without using OSCAR3) in Chemical blogspace has been low. Fortunately, many more people use links to Wikipedia to identify the molecules that talk about.

Last year the Programmeerzomer.nl sponsored one summer student to work on Bioclipse (see the announcement). The Programmeerzomer is much like the Google Summer of Code where I mentor Alexandr. However, it is much smaller and oriented at just the NL area: both the student and the mentor needs to be Dutch, but the opensource project does not.

While looking up a reference for FirstGlance in Jmol, I found Janocchio, a CDK and Jmol based tool for prediction of coupling constants, recently published in Magnetic Resonance in Chemistry. It’s written by Evans, Bodkin, Baker and Sharman (from Eli Lilly) and licensed LGPL. It is one of those rare contributions of pharmaceutical industry, and I can only deeply appreciate this contribution.

Some 7 years ago, following successes in physics, ChemWeb.com launched the Chemistry Preprint Server (CPS), and Warr evaluated it in a JCIM article three years later. She wrote about ‘lessons learned’, but the only one seemed to have been that chemistry was not ready for it, as the project shutdown in 2004. The archives are still available, fortunately, and you may find it amusing to look up my or some other submission.

Dealing with scientific literature has been one important theme in Chemical blogspace. For example, ranking articles and how to store your personal PDF archive has been topics of discussion. In this blog I will summarize bits of the discussion, and my personal view on things. Searching Searching literature is traditionally done in systems like Chemical Abstracts and Web-of-Science.

I just finished setting up a Blue Obelisk section for Chemical blogspace, as future replacement for the current Planet Blue Obelisk (unless someone wants to take over that webpage). The only thing really missing is a RSS feed for recent posts for just the Blue Obelisk member blogs (BTW, just email me if you want to be listed as BO member with your blog too;

Now that my CUBIC desktop machine is shutting down, I made the necessary backups, among a mail.tar for my mail correspondence of about a year. About 500MB in size for almost 8700 files. Strigi is a perfect tool to help me find messages in this archive, as it will recurse into the .tar archive, and even into email attachements.

Mitch just launched ChemRank, a website where we can comment on and vote thumbs up or down for scientific articles. Good initiative I think.

Some time ago I wrote a small Perl script to convert a decision tree created with Weka in the ARFF format to Java source code, for use in the ionization potential prediction in CDK. The advantage is that Weka is no longer used are runtime, and that there is no model that needs to be loaded and interpreted. Instead, it is simple Java code that does the work, much faster.

I use Google Analytics to analyze the visitors of my blogs and of Planet Blue Obelisk too. Now, for the past couple of weeks, the webpage of the Journal of Chemical Information and Modeling is showing up as refering site: What is going on here ?!?! This is really no fake, but cannot find an actual link when I visit the journal webpage either… Update : When looking at the logs, it becomes even weirder.