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:

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My worst cited paper: supervised self-organizing maps

Amazing! It actually is the paper (doi:10.1021/cg060872y) with the best graphics! Is it really then, that scientists do not care about looks?! Or is this just the curse of Closed Access publishing?

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Script logs as HTML+RDFa: mix free text reporting with CSV

Richard (Talis) wrote up a three-step tutorial on how to publish your data. I think I would be more than happy if scientists reached step 1. Related, Ola asked me a while ago if I was interested in using the computing facilities of UPPMAX, and I was. But until this weekend I did not have the time or energy to give it a spin. If you are puzzled how the heck I see those two items related, read on :)

3 minute read

Amazon, the Kindle edition is more expensive than the paperback??

I am writing some more educational material on cheminformatics, and wanted to link to some of the handbooks already around. I need the book details in BibTex format, so CiteULike is my primary tool to create such content. One of those books is the book An Introduction to Chemoinformatics by Leach and Gillet. I looked up the ISBN number on Amazon, and then I noted something weird:

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Setting up a local Semantic MediaWiki with RDFIO and SPARQL support

My now former student Samuel is doing a really cool Google Summer of Code project on import and export of RDF from a Semantic MediaWiki server. His screencast of today shows very nicely where things are going!

2 minute read

RDFaDev: HTML+RDFa development with FireFox

Celso informed me in this old post about an alternative to Operator for RDFa handling in browsers, or Firefox in this case: the RDFaDev add-on. It works quite well, extracts the RDFa, reports common problems, and even allows running SPARQL directly on the web page, all from within a browser pop up window:

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A new CDK default fingerprinter?

The current default fingerprinter in the CDK depends on aromaticity, but that concept is algorithmically difficult to define, and even experimentally there are multiple dimensions to this concept. Moreover, calculating aromaticity is not cheap, as it requires detecting of ring systems. The purpose why aromaticity is actually included is this: people expect a ethenol moiety to match phenol.

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