Peter Corbett from Peter Murray-Rust’s group at the Unilever Cambridge Centre for Molecular Informatics visited Christoph Steinbeck’s junior Research Group on Molecular Informatics at the CUBIC today, and spoke about the status of Oscar3, a chemistry text mining program with the Artistic License.
The Dutch version of the Google Summer of Code, Programmeerzomer.nl, announced today the five students participating. I was happy to see that Rob Schellhorn was selected with his project proposal for a Ghemical plugin for Bioclipse. Like in the Google original, both the student and the mentoring organization are funded, 3600 and 400 euro respectively.
Together with Christoph, Christian and Jerome, I will be representing the Blue Obelisk movement on the first First Workshop on Chemoinformatics in Europe with the topic Research and Teaching . Though I wonder what this theme excludes? Development? Can’t imagine that commercials companies will not be represented as usual. Moreover, it will likely include some bioinformatics too, unless you consider that to deal with sequences only.
Yesterday I installed the Eclipse Web Tools Platform again, and now succesfully, using the Eclipse update mechanism, on my Kubuntu dapper eclipse install. Because it has a validating XML editor, the one last thing I still needed jEdit for. (I do miss the vertical selection feature of jEdit, though.) It signals me of errors, and allows autocompletion.
November last year, I reported my plans to develop a live CD with all our favorite chemo- and bioinformatics software. Bioclipse requires Java5 and sort of still depends on the Sun JVM (I will experiment with classpath-generics later), but is now distributable with operating systems.
Timo Hannay blogged in Nature’s Nascent blog about the Open Text Mining Interface (OTMI), which is “a suggestion from Nature about how we might achieve text-mining and indexing purposes”. The idea is that each article has a link pointing to a machine readable file containing raw data about (and from?) the article.
I have not blogged for about a week now, and been too busy with other things, like finishing my PhD articles/manuscript, my new job at the CUBIC where I continued the work on proper protein support in Bioclipse using the CDK and Jmol: The latter involves getting the CdkJmolAdapter , the interface between the CDK and Jmol, updated for changes since the Jmol as 3D viewer for CDK article in CDK News , the open
Bioclipse 1.0 is to be released in May, and the cartoon on script command is still not working in the Jmol viewer. For those who do not know yet, Bioclipse is a cool Eclipse RCP based Java chemo-and bioinformatics workbench. To have a better idea what goes on inside Bioclipse, I wrote a new BioPolymer tree to show me the strands in the protein.
As of April 3, I will be working as postdoc in the group of Christoph Steinbeck at the Cologne University BioInformatics Center, or simply CUBIC, for a year. Though no exact plans have been decided upon, the work will include CDK, CML, ontologies, Bioclipse, semantic web technologies, Jmol, and other interesting things. Research areas will at least include QSAR, but I hope to touch bits of bioinformatics too.
With quite some help from Ola (thanx!), I made good progress with the CMLRSS plugin . The current result looks like: A problem in the transition from Jumbo 5.0 to 5.1 is causing a problem so that it does not show a 3D model or 2D diagram, but that will follow soon.