chem-bla-ics

In reply to interesting comments to my previous blog on Strigi and xAttr support in KDE4, I would like to suggest the following mockups, which I would find very useful. The deal with the ability to store keywords, for example, not but necessarily using xAttr. I have no idea on how to implement these mockups, so any help or pointers are appreciated.

The first plot is an example of how these keyword markup could be used in KDE, other than searching itself.

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. Oscar3, the successor of version 1 and 2, can detect and extract molecular structures and experimental details from plain text articles, using a variety of text mining techniques.

With some help, I got the kfile stream analyzer for Strigi working. This means that Strigi will now index the meta data fields defined by the kfile-chemical plugins.

The problem why it was not working earlier, was that it segfaulted on every creation of KDE classes. That's something I really hate about C/C++: the lack of stack traces, though valgrind was helpful. It turned out that adding the below line fixed all.

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.

Desktop searching has become a hot topic (some earlier blogs), now that years of data accumulated on ones hard disk: PDFs, OpenOffice.org documents, Latex manuscripts, old Java source code, digitized music, and a lot of chemical files. Well, on my hard disk that is. Unlike piles of paper, a computer could search this data, but due to the size an index is required.

Just wanted to make sure this news made it to the Blue Obelisk Planet too: David Strumfels reported that he extended MS-Excel with CDK functionality.

Recent Developments of the Chemistry Development Kit (CDK) - An Open-Source Java Library for Chemo- and Bioinformatics discusses (reasonably) recent additions to the CDK. It appeared in issue 17 of this years Current Pharmaceutical Design volume, after being too long in the queue after being accepted; but I am happy that it is out now.

The article discusses CDK's QSAR capabilities (the class designs and an overview of provided descriptors), the 3D model builder (see also C.