XHTML+RDFa: chemical examples

Steffen asked me if I could also provide a few examples on how to actually put RDF triples in the HTML, as the template I gave yesterday is a mere empty canvas to draw the triples on. There are actually various examples in my blog, which I will summarize here. 4 minute read

XHTML+RDFa Template

There was some more discussion on machine readability of notebooks again, something I have blogged about for a long time now. less than 1 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

Cleaner CDK Code #8: the Java Naming Conventions and Camel Casing

Another simple approach to make your code more readable, is to adhere to the Java naming conventions. They prescribe that variables start with a lower case characters, as do method names. Class and interfaces, however, start with upper case characters. By all using these same conventions, we need to learn only one scheme and can more easily recognize what are variables, methods and classes. Have a look at these naming conventions by Oracle and the concept of Camel Casing, heavily used in Java. 1 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

Cleaner CDK Code #7: understand what the code is supposed to do

It has been a while since I posted a blog post in this series (see below for a full list so far), but was fixing a problem for Nina (OpenTox), and found some code I did not understand. So, here’s another useful tip (IMHO) for writing CDK code. Well, in particular, patching CDK code in this case. 3 minute read

Using Bioclipse to upload data to an OpenTox server

As part of a continuing mashup of Bioclipse and OpenTox, I sat down with Nina in Oxford to implement uploading molecules from within Bioclipse with JavaScript to OpenTox servers. This opens the route to calculate QSAR descriptors using the OpenTox API. less than 1 minute read