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Text mining for chemistry using OSCAR3
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.
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Strigi gets kfile plugin support
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.
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Dutch Summer of Code sponsors a Bioclipse project
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.
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KDE desktop search: Kat, Strigi and Tenor
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. What’s KDE4 going to offer?
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A chemistry extension for spreadsheet(s)
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 . I wonder how difficult it would be to do this with Kspread or Gnumeric?
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Recent Developments of the Chemistry Development Kit
Recent Developments of the Chemistry Development Kit (CDK) - An Open-Source Java Library for Chemo- and Bioinformatics (green OA) 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.
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Blue Obelisk in Obernai at Chemoinformatics in Europe
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.