Groovy Cheminformatics...

Update: the fourth edition is out. 1 minute read

GitHub Tip: download commits as patches

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. less than 1 minute read

The 9th International Conference on Chemical Structures (ICCS)

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Karolinska Institutet

Hi all, and a happy 2011! After a turbulent December (finishing up in the Oscar project), holidays, etc, I am starting to get some sense of organization in my new position at the Institutet för miljömedicin at the Karolinska Institutet in Stockholm. I will be using cheminformatics and chemometrics methods in toxicology studies, and work in the groups of Prof. Roland Grafström and Prof. Bengt Fadeel. less than 1 minute read

The 100th Blue Obelisk 2006 paper citation

Two and a half months after the CDK milestone, the Blue Obelisk paper also reached 100 citations. Here the lucky paper is Design, Synthesis, and Preclinical Evaluation of New 5,6- (or 6,7-) Disubstituted-2-(fluorophenyl)quinolin-4-one Derivatives as Potent Antitumor Agents by Chou et al (doi:10.1021/jm100780c). The Blue Obelisk paper (doi:10.1021/ci050400b) is cited because the authors used OpenBabel. About half of the 100 citations is because OpenBabel was used, whereas OpenBabel is only mentioned as one of the Blue Obelisk-associated unprojects in the Blue Obelisk paper. less than 1 minute read

Text mining chemistry from Dutch or Swedish texts

Oscar is a text miner. It mines in text for chemistry. Oscar4 is the next iteration of Oscar code that I worked on in the past three months, with Lezan, Sam, and David. I blogged about aspects of Oscar4 at several occasions: 3 minute read

Blogging as part of your workflow

Today is the last day I work on Oscar in my position in Cambridge (tomorrow I have a day off and fly back to Sweden). Three months go quick indeed. Next Monday I start my position in Stockholm at the IMM department at the Karolinska Institutet on predictive toxicology. Back in Sweden, it is. Well, of course, I worked from home most of the time anyway. 1 minute read