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Cleaner CDK Code #7: understand what the code is supposed to do
It has been a while since I posted a blog post in this series (see below for a full list so far), but was fixing a problem for Nina (OpenTox), and found some code I did not understand. So, here’s another useful tip (IMHO) for writing CDK code. Well, in particular, patching CDK code in this case.
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Using Bioclipse to upload data to an OpenTox server
As part of a continuing mashup of Bioclipse and OpenTox, I sat down with Nina in Oxford to implement uploading molecules from within Bioclipse with JavaScript to OpenTox servers. This opens the route to calculate QSAR descriptors using the OpenTox API.
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Is there an Open Specification for structure normalization?
Over at the Blue Obelisk eXchange, I just posted this question:
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Oxford...
Yesterday, I arrived in Oxford, after a 3.5 hour bus transfer from London Stansted. Long, boring ride (though I might have seen a few red kites, but seeing that they were near extinct, I am wondering what other large bird of prey has strong split tail like a swallow). Showed once more that the UK infrastructure has hardly changed since the 19th century. Enjoying an undergraduate room at one of the colleges. Pretty basic, but makes me feel more like a human than a tourist. Yes!, undergraduate students are human too! One of the advantages is you get an excellent internet connection :)
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CDK 1.2.6: the changes and the authors
Like all release in the 1.2 series after CDK 1.2.0, release 1.2.6 is a bug fix release. Anyone running a CDK 1.2 version is advised to upgrade. New in this release is the availability of a torrent for the cdk-1.2.6.jar (see BitTorrents for Science). Please find below the changes and the authors that contributed to this release.
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An Ubuntu Blue Obelisk meta package
There was some talk recently about Blue Obelisk software available as Ubuntu / Debian packages. This morning I had trouble waking up, so hacked up a metapackage, so that you can now do:
