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Multiple inheritence for content types?
Bioclipse is an environment for handling and processing life sciences data. This data is present in files with a wide variety of formats, each of which can contain a particular data type. For example, a we can have a single molecule in MDL molfile and in CML.
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Rednael, CDK Git for Rajarshi's patches, PubChem SDF
Short blog item about some CDK Git updates. Could not get sleep, so might as well spend that time on CDK hacking, not? Reason why I actually could not catch sleep was the news that PubChem SD files are not regular MDL SD files, but use custom extensions, for example, for dative bonds (see this PDF). This surely explains the weird things I have seen, but, unfortunately, the big SDF button on PubChem does not warn about that. Anyway, thanx for Wolfgang for informing about that customization!
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Groovy CDK and the Keyword List
Today I have been hacking a bit more on the CDK material for the CDK workshop (see CDK - The Documentation). Below are two previews, one with a LaTeX-ified keyword list (here as HTML):
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"Open Knowledge: Reproducibility in Cheminformatics with Open Data, Open Source and Open Standards"
I have submitted today the abstract of my talk at the GDCh-Wissenschaftsforum Chemie 2009 in Frankfurt in August as part of the Open Notebook Science/Open Drug Discovery session:
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StARlite talks in Uppsala; Helena's Open Chemogenomics thesis
John was in Uppsala last Friday, and our group had the pleasure of talking to/with him before he was opponent to Helena defending her thesis on Chemogenomics: Models of Protein-Ligand Interaction Space (ISBN:978-91-554-7430-0). Since we believe we can do tons of really interesting science on John’s StARlite data, I was excited to talk to him in person. He gave three talks that day, and managed to keep the overlap minimal (yes, not quite an absolute measure, but you get the point). We showed him the efforts of Arvid, Carl, Jonathan and me on converting the StARlite data to RDF, on which I will write shortly.
