JChemPaint update: merging of patches and CDK statistics

With the JChemPaint workshop just passed, there is much work from UU and the EBI to be integrated. Moreover, Rajarshi just merged a lot of fixes from CDK 1.2.x into the master branch, which will be a big rebase too. That said, I need to do this to recalculate source code statistics for the CDK.

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My HTML+RDFa homepage

Finally got around to adding a few more bits to my new science homepage: egonw.github.com. Cool thing about this new page is that it is HTML+RDFa, so, my new FOAF profile is embedded in the HTML:

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Really free chemistry books

With pleasure I read Analogue or Digital? - Both, Please. Funnily, I just created MP3 (or, preferably Ogg Vorbis, superior but hardly any support by commercial companies, who rather seem to pay license fees) directly from the CD.

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VRMS meme: how much non-free software are you running?

Over at Planet Ubuntu there is a meme running around VRMS (Virtual Richard M. Stallman, brilliant name!) which finds non-free software on your desktop. I uninstalled Sun’s Java6, for which there is the OpenJDK6 alternative.

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Bioclipse, RDF and defeasible reasoning

Well, I have yet to read the paper in detail, but my new student Samuel is going to work for 20 weeks on defeasible reasoning with DrProlog in Bioclipse.

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Open Chemical Data #1: NMRShiftDB

As I reported earlier, progress is only possible of you can modify and redistribute. This is why Open Data, Open Source, and Open Standards are so important to us Blue Obelisk members. For data, proper licensing makes these two requirements possible, but more importantly, make those rights explicit. Rich is running the nice Zusammen blog, but most of his entries are not Open Data. Even larger chemistry data repositories can be vague and have seemingly contradicting statements.

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The Art of Programming: do not leak implementation details

At the JChemPaint workshop here in Uppsala, where we have Mark from Chris’ group as our guest, we encountered an inconsistency in CDK 1.2, where the bond stereochemistry did not yet follow the pattern recently adopted of having Class fields, to allow using null to have the semantics of undefined. Previously, the defaults for native values were confounded with set values. For example, the formal charge unset and 0 would be have a field value int = 0.

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