CDK-Taverna: an open workflow environment for cheminformatics

Thomas Kuhn, Egon L. Willighagen, Achim Zielesny, Christoph Steinbeck*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

37 Citations (Web of Science)

Abstract

Background: 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.

Results: 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.

Conclusions: 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.

Original languageEnglish
Article number159
Number of pages11
JournalBMC Bioinformatics
Volume11
DOIs
Publication statusPublished - 29 Mar 2010
Externally publishedYes

Keywords

  • SOURCE JAVA LIBRARY
  • DEVELOPMENT KIT CDK
  • CHEMICAL MARKUP
  • WEB
  • XML

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