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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Running R from within Bioclipse

 

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In Silico Toxicology

Today my copy of In Silico Toxicology: Principles and Applications (Issues in Toxicology) arrived at the local Library. Library with a capital L: we requested the book 1.5 weeks ago, got confirmation it got ordered last week Monday, and just picked it up. Well done!

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Extracting 3D coordinates from PDB files with Groovy CDK

BioStar featured a question today about how to extract 3D coordinates from PDB files . Now, a simple script may actually do, and BioJava was mentioned too . Of course, it can also be done with the CDK . For example using this Groovy code:

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GitHub Tip: download commits as patches

Some time ago, the brilliant GitHub people gave me the following tip. Rajarshi is lazy, and might find it interesting. By appending .patch to the commit URL, a commit can easily be downloaded as patch. That way, developers can easily download it with wget or curl and apply it locally with git am, without having the fetch the full repository.

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