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CDK-Taverna: an open workflow environment for cheminformatics

Thomas Kuhn1, Egon L Willighagen2, Achim Zielesny1 and Christoph Steinbeck3*

Author affiliations

1 Institute for Bioinformatics and Cheminformatics, University of Applied Sciences of Gelsenkirchen, Recklinghausen, Germany

2 Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden

3 Chemoinformatics and Metabolism, European Bioinformatics Institute (EBI), Cambridge, UK

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Citation and License

BMC Bioinformatics 2010, 11:159  doi:10.1186/1471-2105-11-159

Published: 29 March 2010



Small molecules are of increasing interest for bioinformatics in areas such as metabolomics and drug discovery. The recent release of large open access chemistry databases generates a demand for flexible tools to process them and discover new knowledge. To freely support open science based on these data resources, it is desirable for the processing tools to be open source and available for everyone.


Here we describe a novel combination of the workflow engine Taverna and the cheminformatics library Chemistry Development Kit (CDK) resulting in a open source workflow solution for cheminformatics. We have implemented more than 160 different workers to handle specific cheminformatics tasks. We describe the applications of CDK-Taverna in various usage scenarios.


The combination of the workflow engine Taverna and the Chemistry Development Kit provides the first open source cheminformatics workflow solution for the biosciences. With the Taverna-community working towards a more powerful workflow engine and a more user-friendly user interface, CDK-Taverna has the potential to become a free alternative to existing proprietary workflow tools.