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! 1 minute read

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): less than 1 minute read

"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: 1 minute read

Nature Jobs - Google Map mashup

Nothing much I need to say about the NatureJobs Interactive World Map, I think. Thanx to Partial Immortalization for the link on FriendFeed! less than 1 minute read

CDK - The Documentation

In preparation for the CDK workshop later this month, I am writing up my material for my kick-off presentation of the workshop. So, I better make it good. Using LaTeX at least overcomes my laziness which always made Word documents look stupid. Even default LaTeX looks good: 1 minute read

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. 1 minute read

Highlighting Console output in Eclipse with Grep Console

I ran into an Eclipse Grep Console plugin (EPL license) today that takes regular expression to color output in the Console. Given the amount of output Bioclipse and the CDK give when in DEBUG mode, this allows me to highlight those bits I am interested in. For example, comments on the Bioclipse managers: less than 1 minute read