CDK-Taverna paper published

It took a while, but the CDK-Taverna paper (doi:10.1186/1471-2105-11-159) which has been in preparation for a while in the CDK subversion repository, is now published. Christoph already wrote up a brief explanation in his blog: 1 minute read

Updated my blog template

I noted today that blogger.com, the blog service provider I am using, had new templates. I was getting tired of the old one anyway, so tried the simple template using the usual orange: quite satisfactory! At least, beats buying a book like this Blogger: Beyond the Basics. Don’t have time for that. 1 minute read

Cleaner CDK Code #3: run the PMD tests

PMD is a tool to run some tests against your source code. The check for code style, common problems, and places where code could be improved. The CDK has been using it for years now, such as here for CDK 1.3.x. less than 1 minute read

Oxford, August 2010: eCheminfo Predictive ADME & Toxicology 2010 Workshop

The first week of August I will attend the eCheminfo Predictive ADME & Toxicology Workshop (LinkedIn Event) for which I received a Bursary Award. It will be my first time in Oxford, and I am very much looking forward to it! 1 minute read

Cleaner CDK Code #2: String.contains() and logger messages

Second in the series (see #1), with two rather small tips. less than 1 minute read

RDF-powered QSAR wizard: SPARQL end points providing wizard content

As you know from my blog, one of the things I am working on is to push RDF functionality in Bioclipse, as I believe it to be the missing link between molecular chemometrics and literature, databases, and other non-numerical information sources. 1 minute read

Cleaner CDK Code #1: List<IAtom> and the for-each loop

In a desperate attempt to force me to write on my CDK code snippet book, I’m going to write some code tips to create clear code. Hopefully, this is useful for people writing patches and reviewers alike, too. 1 minute read