My team at the EBI maintains a couple of databases [1,2,3] dealing with various aspects of (bio-) organic chemistry. All of them need chemical structure editor applets where users can specify queries for substructure searches and which are used by our curators for data entry.The development of these databases is funded by the European Union […]
The CDK workshop 2009 is over and what is left is a bad cold. But I’ll get over it. The workshop itself was phantastic – we had 40 participants with well balanced contributions from industry and academia. The first half day was dedicated to tutorials on various aspects of CDK, basic installation, our CDK and […]
Oliver Karch from Merck-Serono gave the last talk on Tuesday morning, showing how to visualize CDK to visualize molecular spaces in a way “as easy as Google Earth”. They us a workflow with Pipeline Pilot, a MolWind Server, which is Java and Apache based and then render 2D structures with CDK. The NASA Molwind client […]
In the second research talk on Tuesday morning Asad from EBI talks about his research on finding pathes in metabolic networks. Asad and I have been working together CUBIC in Cologne and are now again colleagues at EBI. Goal of his work has been to find patterns in biological reaction networks. His first examples deals […]
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 […]