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Creating chemo- & bioinformatics workflows, further developments within the CDK-Taverna Project

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The CDK-Taverna project aims at building an open-source pipelining solution through combination of different open-source projects such as Taverna [1], the Chemistry Development Kit (CDK) [2] and Bioclipse [3].

Pipelining or workflow tools allow for the Lego™-like, graphical assembly of I/O modules and algorithms into a complex workflow which can be easily deployed, modified and tested without the hassle of implementing it into a monolithic application.

Current developments in CDK-Taverna focus on a soft computing framework which allows a flexible use of different methods from, for example, the WEKA [4] library. Here, properties of chemical substances may be calculated using descriptors from the QSAR / QSPR package of the Chemistry Development Kit (CDK).

Further, a reaction enumeration algorithm for combinatorial chemistry based on existing methods of the Chemistry Development Kit is being developed. This algorithm allows for the enumeration of a reaction given that reactants and products are provided as “Markush” structures.


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    Oinn T, Addis M, Ferris M, Marvin D, Senger M, Greenwood M, Carver T, Glover K, Pocock M, Wipat A, Li P: Taverna: A tool for the composition and enactment of bioinformatics workflows. Bioinformatics. 2004, 20 (17): 3045-3054. 10.1093/bioinformatics/bth361.

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    Steinbeck C, Han YQ, Kuhn S, Horlacher O, Luttmann E, Willighagen E: The Chemistry Development Kit (CDK): An open-source Java library for chemo- and bioinformatics. J Chem Inf Comput Sci. 2003, 43: 493-500. 10.1021/ci025584y.

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    Spjuth O, Helmus T, Willighagen EL, Kuhn S, Eklund V, et al: An open rich client workbench for chemo- and bioinformatics. submitted.,

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Correspondence to Thomas Kuhn.

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Kuhn, T., Zielesny, A. & Steinbeck, C. Creating chemo- & bioinformatics workflows, further developments within the CDK-Taverna Project. Chemistry Central Journal 2, P27 (2008) doi:10.1186/1752-153X-2-S1-P27

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  • Chemical Substance
  • Soft Computing
  • Chemistry Development
  • Current Development
  • Computing Framework