Royce Murray and Caveat Emptor

Derek’s blog pointed me to an editorial by Royce Murray Science Blogs and Caveat Emptor (doi:10.1021/ac102628p). He is warning us, science scholars, for blogs. He is accusing bloggers for not being scholarly, not checking facts etc.

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Working on Oscar for three months

As Peter announced in his blog, and I tweeted earlier, I have started as postdoctoral research associate in Peter’s group at the University of Cambridge, to work the next three months on Oscar, a chemical text mining tool. My tasks will focus on programmatical plumbing instead of method development, and I am aiming at integration with CDK-Taverna (see doi:10.1186/1471-2105-11-159, and which is currently being ported to Taverna 2.2 by Andreas). Sam and Lezan having been working on the refactoring as well, and will help me out with the gory details of the current code.

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Are these organic molecules the same?

Cambridge pubs are not just good for the (Danish) beer, but also for the pub quizzes. Peter asked if the below molecules are the same. I did not think so, but… what do you think? He also asked if they are chiral. We got until tomorrow 20:00 BST.

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Mapping BioStar users onto the world map

Neil is my new bioinformatics hero! (Sorry Pierre :)

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CDK Book in progress

Very much overdue, but still in progress, is my book on CDK programming. I am in love with the writing environment, a mix of make, Groovy and LaTeX, where the code snippets are written in Groovy and embedded into LaTeX (see CDK - The Documentation). The Groovy script is actually run by the build system, allowing me to embed the output too.

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The 100th CDK 2003 paper

We got a winner! Crabtree just published the paper An Open-Source Java Platform for Automated Reaction Mapping (doi:10.1021/ci100061d), and is, according to Web of Science, the 100th paper to cite the CDK 2003 paper (doi:10.1021/ci025584y)!

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RDFa support in CiteULike

Last month I reported a A list of things I miss in CiteULike and the developers have not been sitting still. Only one of the things they started to adopt is RDFa in the CiteULike web interface. Of course, you will not see this in the browser, unless you use something like the RDFaDev plugin in Firefox:

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