I reported earlier how to I uploaded the ChemPedia (RIP) data onto Kasabi. But for ChEMBL-RDF I have used the pytassium tool, not just because it has a cool name :) I discovered yesterday, however, that I did not write down in this lab notebook, what steps I needed to take to reproduce it. And I just wanted to uploaded new triples to the ChEMBL-RDF data set on Kasabi.

Almost a year ago I started a position with Peter Murray-Rust to work on Oscar for three months (see this overview of results; a paper by the full Oscar team (Sam, David, Dan, Lezan) is pending, and I’m really happy to have been able to contribute bits to the project). Since then, I have had little time :( That’s how it goes, with post-hopping, unfortunately. One thing I did do after that, was write a Bioclipse plugin.

About two weeks ago, the ChemConnector blog reported an InChIKey collosion detected by Prof. Goodman . Unlike the previous collision, this one was based solely on the graph and not on stereochemistry.

Web of Science is my de facto standard for citation statistics (I need these for VR grant applications), and defines the lower limit of citations (it is pretty clean, but I do have to ping them now and then to fix something). The public front-end of it is Researcher ID. There is an Microsoft initiative, which looks clean but doesn’t work on Linux for the nicer things, but the coverage of journals is pretty bad in my field, giving a biased

Update : the fourth edition is out. I am starting to get the hang of this publishing soon, publishing often thing, and just uploaded edition 1.4.1-0 of the Groovy Cheminformatics book. The cover is the same (with one typo fix), and the content is 20 pages thicker. True, six of those pages are isotope masses of all natural isotopes.

I cannot find the bug report just now, but the CDK has an open problem with change even notification, where the nonotify classes still caused change event to be sent around.

Kasabi is a new, RDF hosting service by Talis. It’s still in beta, and I have been testing their beta service with the RDF version I created of ChemPedia Substances (the now no longer existing cool web service from MetaMolecular to draw and name organic molecules).

Julio and Gert placed their ICCS 2011 work online, and today I was going through old CDs (see From the archives: Chemical Web, and the CDK in 2004 and Chiral Molecules: how cool is the SEM picture?). I also ran into my ICCS 2005 poster, and because that too was before I started blogging, I never posted it online.

Update 2021-02: this post is still the second-most read post in my blog. Welcome!

Update : the fourth edition is out. Some project are never finished.

Some time ago, the brilliant GitHub people gave me the following tip. Rajarshi is lazy, and might find it interesting. By appending .patch to the commit URL, a commit can easily be downloaded as patch. That way, developers can easily download it with wget or curl and apply it locally with git am, without having the fetch the full repository.