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Friday, September 21, 2012

EBI visit: CDK hacking and bioassays

This week I visited the EBI for a set of meetings, among which a CDK hackathon (results will follow later), a Blue Obelisk (doi:10.1186/1758-2946-3-37) pub meetup, and discussions about bioassays. The latter involved a Open PHACTS (doi:10.1016/j.drudis.2012.05.016) specific meeting where we talked about assay data and about such in ChEMBL and ChEMBL-RDF, and me attending a EU-OPENSCREEN meeting on invitation from Janna Hastings.

The whole week was brilliant, and we made good progress on many fronts, and it got even better because Janna gave me 15 minutes to talk about Open Science. I touched on various aspects, and showed the CDK, OrChem (doi:10.1186/1758-2946-1-17), KNIME, Bioclipse and the Brunn (doi:10.1186/1471-2105-12-179) use case, the network of Blue Obelisk projects (and several showed up during presentations at the EU-OPENSCREEN meeting, including RDKit, Open Babel/PyBel (doi:10.1186/1758-2946-3-33), Cinfony (doi:10.1186/1752-153X-2-24), JChemPaint (doi:10.3390/50100093), the Linked Open Drug Data project of the HCLS ig (doi:10.1186/1758-2946-3-19), Open PHACTS, WikiPathways, PathVisio, SEURAT-1, OpenTox (doi:10.1186/1758-2946-2-7), and ToxBank.

I will add links to papers and websites in the blog post later, but wanted to put the slides in my blog before I catch the taxi to the airport in 20 minutes :)


I had particular good responses on the Blue Obelisk community, where we managed to get a rich eco-system of open source cheminformatics tools. This was one of the things I stressed in my presentation, that it is more practical to not try and make one solution, but have all solutions interoperate. Look what that has brought cheminformatics (click the image for all details):