SteinBlog

Archive for the ‘Chemistry Development Kit’ Category

Internship in Bioinformatics/Cheminformatics

We are looking for a candidate for an internship/trainee position in bioinformatics/cheminformatics at the European Bioinformatics Institute (EMBL-EBI) to work on a high-performance generator for chemical structures. This position requires strong programming skills in Java, a reasonable working knowledge in chemical structures and graph theory as well as an interest in learning about Apache Hadoop […]

CDK-Taverna paper published

We are glad to announce that our article about CDK-Taverna, an open workflow solution for cheminformatics, is now online on BMC Bioinformatics. CDK-Taverna, which lives at http://www.cdk-taverna.de/, features more than 160 workers for various tasks in molecular informatics. The workflow paradigm allows scientists to flexibly create generic workflows using different kinds of data sources, filters […]

What do we expect from a chemical structure editor applet?

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 […]

CDK Workshop 2009 Wrap-up

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 […]

John van Drie’s talk on CDK in Virtual Drug Discovery

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 […]

Ola Spjuth talks about “Accessing and scripting CDK from Bioclipse”

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 Rijnbeek’s talk about CDK and databases

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 […]