Some time ago I wrote a small Perl script to convert a decision tree created with Weka in the ARFF format to Java source code, for use in the ionization potential prediction in CDK. The advantage is that Weka is no longer used are runtime, and that there is no model that needs to be loaded and interpreted. Instead, it is simple Java code that does the work, much faster.
I use Google Analytics to analyze the visitors of my blogs and of Planet Blue Obelisk too. Now, for the past couple of weeks, the webpage of the Journal of Chemical Information and Modeling is showing up as refering site: What is going on here ?!?! This is really no fake, but cannot find an actual link when I visit the journal webpage either… Update : When looking at the logs, it becomes even weirder.
I just read on Planet Blue Obelisk Peter’s disturbing news (via Suber) that Wiley thinks it can copyright a set of numbers (also known as data). That is a sad milestone in scientific publishing. It reminds me of the recent internet hype about a long number recently flooding the internet (and notably del.icio.us) related to watching DVDs you legally bought.
Getting back on microformats (see yesterday), I added my hCard to the bottom of my blog: I will likely populate it a bit more soon (after holiday in Sweden). Now, if you had the Firefox plugin Operator installed, you would have my contact information show up in your FF toolbar, like this: Note the ‘Export Contact’ button in the toolbar.
Peter blogged some days ago about microformats and how they could be used in chemistry. Being late and a bit absent minded, I added a short comment that Chemical blogspace supports microformats for chemistry, and that chemistry is harvested from that, and actually semantically distributed again using CMLRSS.
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.