Bioclipse upgraded to CDK 1.3.8 and CDK-JChemPaint 17: builds broken

Yesterday I did some boring plumbing: I upgraded our GC/MS machines with new hardware. Well, the cheminformatics equivalent of it anyway. I upgraded the Bioclipse bundles in org.openscience.cdk for CDK 1.3.8 and CDK-JChemPaint 17. This is typically a painful process, and now even more because a lot is changing with how Bioclipse is build, which is with Buckminster on Bioclipse’ Hudson server. I am happy that Arvid is doing the digging into Buckminster, as automatic building of Eclipse-RCP tools is straightforward. Each part is describes by, seemingly, at least five configurations files. For each plugin we have plugin dependencies, plugins are wrapped into features, where you can get dependencies wrong too, and update sites, which need to be in shape too. And on the Buckminster-side there are .rmap and .cquery files pointing to the right git repositories, each of which you can get wrong too.

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Chemical data curation: yes, it is that bad.

The readers of Antony’s blog know enough about the problem. And many in the QSAR community know it too (and many other do not). Chemical structure data is noisy. I haven’t recently created a new local data set for analysis, so I have not taken time to blog about it much, but the ambiguity in chemical databases is enormous. Just yesterday, Antony and I had a good discussion about tautomers and in particular how things are linked together.

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Groovy Cheminformatics...

Update: the fourth edition is out.

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Accessing Google Spreadsheets from Bioclipse

 

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Open Chemical Data #2: Dryad

Nico asked recently about the availability of chemical data as RDF. There is no so much really. Finding large amounts of Open Data in chemistry is in general a problem. Things are slowly changing, however, though it is not very apparent.

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Integrating CiteULike in LaTeX-based paper writing

Just a quick note. I started using CiteULike as replacement for JabRef (I hope that it will abstract the backend interface, allowing CiteULike to act as online store), and picked up an idea from someone to use groups for individual papers I am working on. And, I extended my Makefile (Marcus, yeah, I know I should use cmake :) to download the references in the group in BibTeX format:

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DIY: Running R from within Bioclipse

Important: this blog post is about a development version of Bioclipse, not about the stable 2.4 series. See also Gilleain’s comment for this post.

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