John has started his talk this morning by giving a manifesto for open source in drug discovery. He gives an introduction to the history of virtual drug discovery, starting in 1985 (showing some dinosaur computers :-)) and then quickly jumps to y2k. While the hardware has dramatically fallen in price, the drug discovery software still […]
Our friends from Konstanz present their KNIME workflow solution which contains the CDK for achieving cheminformatics functionality.We have a long-standing collaboration with them to help them to get CDK working in KNIME. Unfortunately, we are still at cdk 1.1 in KNIME where a number of issues prevent CDK/KNIME to perform really well.With an integration of […]
Our friend Ola Spjuth from Uppsala talks about how to access CDK from within Bioclipse using Bioclipse’s built-in scripting capabilities. Ola will cover Bioclipse The Use of CDK in Bioclipse Scripting in Bioclipse Calculating CDK properties First we’ll download Bioclipse 2.0Beta4 from http://www.bioclipse.net. Ola continues by explaining Bioclipse’s component architecture. For the tutorial part of […]
Mark is working in my group on a CDK-based plugin for Oracle to enable chemistry searching: Similarity and Substructure. In his talk at the CDK workshop, he points out in the beginning that this is not a cartridge as defined by Oracle. It is a set of java classes loaded by the Oracle Java virtual […]
After my opening talk at the CDK workshop, Egon Willighagen gave an introduction on how to get started with the CDK. He uses the scripting environment Groovy to demonstrate things. Egon has prepared a LaTeX document with his teaching material as well as the code examples on at http://pele.farmbio.uu.se/groovy. Turns out that Groovy scripting is […]
I’m collecting some thoughts for my CDK workshop kick-off talk on Monday and I guess I’ll go for the boring regular version, with an introduction to CDK history, followed by some statistical figures and ending with an explanation of the format for the developers workshop on Tuesday afternoon. As anyone can read on our CDK […]
I’m attending the 3rd International Biocuration Conference in Berlin, which looks like a pretty successful meeting in terms of numbers of participants. Seems like somewhere between 100 and 200 participants. It looks like the time for recognition for biocuration and curated biological resource has come. The International Society for Biocuration has been inaugurated yesterday. People […]
I’ve been invited to present our ChEBI ontology at the 2009 Fall Meeting of the American Chemical Society. Here is our abstract: ChEBI – An open ontology for Chemical Entities of Biological Interest Paula de Matos (1), Kirill Degtyarenko (2), Marcus Ennis (1), Janna Hastings (1), Inma Spiteri (1) and Christoph Steinbeck (1) (1) European […]
I’ve just arrived at the ACS meeting in Salt Lake City. The trip was a real nuisance, 19 hours or so, and I always ask myself why I do this stuff.Still, after a fantastic breakfast in my even more fantastic hotel, the Grand America Hotel (review pending), and now being at the meeting, is is […]
I’m delighted to announce that the first open access journal of our field, the Journal of Cheminformatics, is now live and has published its first articles. Journal of Cheminformatics is a new open access journal from Chemistry Central publishing peer-reviewed research in all aspects of cheminformatics and molecular modelling. It is run by Editors-in-Chief David […]