Oscar text mining in Taverna

One of the goals of my project in Cambridge is to make Oscar available as Taverna plugin (source code, Hudson build). I have progressed somewhat, but still struggling with getting the update site working. The plugin actually installs into Taverna 2.2.0, but the activities do not show up. While this is work in progress, and the other project goal is refactoring, a current demo workflow looks like: 1 minute read

Working on Oscar for three months

As Peter announced in his blog, and I tweeted earlier, I have started as postdoctoral research associate in Peter’s group at the University of Cambridge, to work the next three months on Oscar, a chemical text mining tool. My tasks will focus on programmatical plumbing instead of method development, and I am aiming at integration with CDK-Taverna (see doi:10.1186/1471-2105-11-159, and which is currently being ported to Taverna 2.2 by Andreas). Sam and Lezan having been working on the refactoring as well, and will help me out with the gory details of the current code. less than 1 minute read

A list of things I miss in CiteULike

AJCann posted a blog today about what he doesn’t like about Mendeley. Abhishek replied that he does not like people complain about one tool, instead of pointing out a good alternative. Mendeley has two alternatives, Zotero and CiteULike (there is also Connotea, but got behind in evolution). 2 minute read

The Molecular Chemometrics Principles #3: stand on shoulders

I have blogged about two Molecular Chemometrics principles so far: 1 minute read

The Molecular Chemometrics Principles #2: be clear in what you mean

I noted earlier this week that [d]uring the week [in Oxford ], 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. This triggered the start of a series of principles in the field I coined Molecular Chemometrics, and the promise that I will try to indicate in each blog post to which of these principles it relates. Just to put things in a bit more perspective; to make a bit more clear why I am blogging about that bit; just to be clear in what I mean. 2 minute read

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