After handing in a new draft of my PhD manuscript with my co-promotors last friday, and a week before we leave for Sweden, it is time to start finishing up the material for my one hour workshop on chemoinformatics in general and QSAR/QSPR in particular for the Bioclipse Workshop. Pierre blogged about this movie.

About a year ago Pedro wrote a Greasemonkey script to add comments from PostGenomic.com to table of contents of scientific journals. Noel extended it with support for Chemical blogspace (see also this earlier item). Now, the later website is maintained by me, and I extended the aggregator software with molecule support, for example to show hot molecules on the frontpage (at some point my patches will be backported into mainstream.

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: (Yes, the sun was very bright :) The program was consisted of a couple of group things, like making a short list of articles to write up in the next few months.

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.

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. I would warmly thank everyone who has contributed to the project in one way or another (I worked more on maintainance than implementing functionality), as it has been a great pleasure to make CDK releases.

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’: It seems to use other engine to do the searching and focus on the clustering. Source engine exclude Google, and include Gigablast, MSN and Wikipedia.

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.

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;

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: CINF morning Yeah, more CINF session reports; I’m a chemoinformatician, remember. Chen showed us around in the latest changes in ChemDB, such as retrosynthesis planning. Banik shows a patented method for showing differences in a set of spectra, though his examples were not really impressive;

I was happy to notice just a minute ago that the first blog items covering the ACS meeting are popping up: C&EN has set up a dedicated blog about the meeting, Nature’s Sceptical Caterine wrote she has reached the meeting too, Richard wrote about the scent of bugs in wine (or so), and Kyle won’t make it other than tomorrow. Additionally, Nature is running a coverage of the ACS meeting.

I arrived in Chicago yesterday afternoon. Much warmed than the cold Chicago the ACS promised me, so my winter coat was really not necessary. Is this global warming? Or was the ACS simply wrong? Anyway, very foggy indeed, just like the Chemistry World blog wrote: There were several other Dutch chemists on the plane, among which a few formed postdocs from Nijmegen, who I knew from the time I was still a M.Sc. student in organic chemistry.