Ex-CUBIC get-together

Yesterday and today I was in Cologne to meet with other ex-CUBIC researchers from Christoph’s research group on chemoinformatics (and with Alexandr). Not all former group members where there, but on the other hand we were complemented with Pascal: less than 1 minute read

Bioclipse now allows QSAR descriptor selection

In preparation for the Embrace Workshop for Bioclipse in May, I am working on the QSAR functionality of Bioclipse. A nice extension point got set up some time ago, called DescriptorProvider, and implemented by plugins to allow calculation of one or more descriptors for the selected molecules. Now, the functionality for the resulting matrix has been around for some time too. less than 1 minute read

CDK 1.0: a milestone after 7 year of development

Last night, I released CDK 1.0 as the previous release candidate did not show up new major problems. It is far from a perfect release (see these still TODO’s and Nightly, run by Rajarshi), but the core is pretty solid. 2 minute read

Clustering web search results

The Dutch Intermediair magazine of this week had a letter sent by a reader introducing Clusty, a web search engine that clusters the results. It does a pretty good job for ‘egon willighagen’: less than 1 minute read

CUBIC period is over

The end of the CUBIC has come, and so did the end of my 1-year postdoc in the group of Christoph Steinbeck. It would have been much better if the group could have continued for one or two more years, so that we could harvest the fruit of the work done in the past years. Only having been group member since April 1 2006, I mostly contributed work to Bioclipse (doi:10.1186/1471-2105-8-59), CMLSpect (submitted), and integrating Miguel’s mass spectrum prediction toolkit into SENECA (doi:10.1021/ci000407n) for structure elucidation. The latter topic is rather exciting and when the method shows powerful enough, this will have a major impact on the field of metabolomics. less than 1 minute read

ACS Chicago - Day #3

Tuesday promised to be an interesting day: an interesting ‘Scientific Communication’ CINF session in the morning and early afternoon. And, rather important to me, the Blue Obelisk dinner that night, just after another CINF party, where I chatted with a few others about options of a chemistry equivalent of the Google Summer of Code; who knows what happens this summer, but start thinking about ideas on how to increase the web experience of chemistry journal web pages. 4 minute read

ACS Chicago - Day #2

The wetter was much better today. This is a view on downtown from the walking bridge between Lake Side and McCormick buildings of the conference site: 1 minute read