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Tuesday, April 24, 2012

#NBIC2012: the Chemistry Development Kit in NL

The demos of Bioclipse-OpenTox went well today (tomorrow more opportunity to drop by). Yesterday I installed Ambit2 and the ontology server, and created a plugin with DS-OpenTox configuration for the localhost. Nina told me how to add local (ToxTree) algorithms as 'models' and register them with the local ontology server, allowing Bioclipse-DS to find them (this assumes that the first command creates the first model):

    curl -X POST http://yourhost:8080/ambit2/algorithm/toxtreecramer
    curl -X POST http://localhost:8080/ontology -d \ 
        "uri=http://localhost:8080/ambit2/model/1"

But, tomorrow I will also talk about CDK development in the Netherlands. It is important to know that the CDK stands on the shoulders of libraries earlier developed by Christoph Steinbeck, like his CompChem libraries, which goes back to 1997! I cannot stress enough that his and Dan Gezelter's early Open Source work from those days made it possible for me, as a student, to join the scene. It was a huge honor to found the CDK together with them, back in 2000!

Also many thanx to Miguel who is co-author of the abstract, not present at NBIC2012, but whom has contributed a lot of work to the CDK. From within Christoph's group and from Leiden!

Abstract
The Chemistry Development Kit (CDK) is an Open Source (Lesser GPL) library for cheminformatics, providing key functionality to handle and compute properties of chemical structures. The CDK was founded in 2000 by an international group with a basis in earlier open sources tools, like Jmol and JChemPaint. The CDK is a international, open project, which has had contributions from The Netherlands as early as 1999. It is used in cheminformatics fields like drug discovery, and bioinformatics fields such as metabolomics and toxicology.

This presentation will detail the current functionality of the CDK and how that was used to support methods in published studies, as well as providing an overview of tools that use the CDK as underlying library. Softwares that provide cheminformatics functionality using the CDK include (plugins for) the workflow environments Taverna and KNIME, the graph network analysis software Cytoscape, general tools Bioclipse, rCDK, and many dedicated tools, include MEF and MZmine2, tools used in metabolomics. 

Currently, the CDK is an international, developed project with contributions from many academic and industrial institutes, with core developers at Leiden University, Maastricht University, the European Bioinformatics Institute, the United States, and many others.