The Molecular Chemometrics Principles #1: access to data

The meetings in and around Oxford were great! I already wrote that the Predictive Toxicology workshop was brilliant (see Oxford… #1 ) and Oxford… #2 ), but I also very, very much enjoyed meeting up with Dan and Nico! During the week, someone (name and address is know at the editorial office) commented on the fact that my blog posts are somewhat difficult to follow; that is, it’s often not clear why I am posting what I am posting. 2 minute read

Oxford... #2

The Predictive Toxicology meeting is over. It was a great meeting, by any standard. Very much recommended, and many thanx to Barry for the organization! The meeting was a true workshop, with a mix of presentations and getting work done. I participated in a group that looked at mutagenicity of potential anti-malaria drugs from the datasets of GSK and Novartis recently release as Open Data. We used various tools to predict properties, and plan to make all our results freely available soon. Otherwise, it was also great to meet Nina again (with whom I talked about OpenTox), and to meet other CDK users, including Patrik (SMARTCyp , doi:10.1021/ml100016x) and David (Inkspot). less than 1 minute read

Oxford...

Yesterday I arrived in Oxford, after a 3.5 hour bus transfer from London Stansted. Long, boring ride (though I might have seen a few red kites , but seeing that they were near extinct, I am wondering what other large bird of prey has strong split tail like a swallow). Showed once more that the UK infrastructure has hardly changed since the 19th century. Enjoying an undergraduate room at one of the colleges. Pretty basic, but makes me feel more like a human than a tourist. Yes!, undergraduate students are human too! One of the advantages is you get an excellent internet connection :) 2 minute read

Cb: New Blogs #13

The Cb software is still holding… I jettinsoned the old post cache, which speeded up the processing of blogs considerably, but the system just doesn’t scale right. Yet, Euan has done a great job, and the Cb site has now been online for some three years! Here are some new blogs included in the aggregation and analysis: 1 minute read

GitHub simplifies code review and leaving comments

The workflow here is that the proposed patch gets uploaded to a GitHub branch or fork; the code reviewer is made aware of the patch, and goes to the commit page on GitHub, and hovers over the line numbers and clicks the ‘Add comment’ button and leaves a comment; the reviewer informs the author, and the author updates his patch. less than 1 minute read

Web 2.0 technologies in Student Assessment

Below should show up the wave (that is, if you have a Google Wave account), about a piece I am writing for a course on PhD Supervision I am following. The aim is to dig up old standards and how they apply to Web 2.0 technologies, including wikis, waves, blogs, source code repositories etc. less than 1 minute read

CIP rules #2: parsing @ and @@ from SMILES

I recently wrote about a project for a (partial) CIP implementation. This implementation is in place, and we are working towards setting up an extensive test suite. The data set we had in mind was available as SMILES and as MDL molfile. Now, the latter does not really specify the stereochemistry of the tetrahedral centers, and relies on wedge bonding. Actually, a few years ago Jonathan Brecher wrote up the IUPAC recommendation for the use of the wedge bond for chirality specification (doi:10.1351/pac200678101897), with 74 pages of rules and examples, like the following (copyright by authors or journal; I’m claiming fair use): less than 1 minute read