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Volume 2 Supplement 1

3rd German Conference on Chemoinformatics: 21. CIC-Workshop

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

Chemistry Central Journal volume 2, Article number: P27 (2008) | Download Citation

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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.

References

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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.

  2. 2.

    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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    Witten IH, Frank E: Data-Mining Practical machine learning tools and techniques. 2005, Morgen Kaufmann, San Francisco, 2nd Edition

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    Hassan M, Brown RB, Varma-O'Brien , Rogers D: Cheminformatics analysis and learning in a data pipelining environment. Molecular Diversity. 2006, 10: 283-299. 10.1007/s11030-006-9041-5.

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Author information

Affiliations

  1. Cologne University Bioinformatics Center (CUBIC), Cologne, Germany

    • Thomas Kuhn
    • , Achim Zielesny
    •  & Christoph Steinbeck

  2. University of Applied Sciences of Gelsenkirchen, Institute for Bioinformatics and Chemoinformatics, Recklinghausen, Germany

    • Thomas Kuhn

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Corresponding author

Correspondence to Thomas Kuhn.

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Open Access This article is distributed under the terms of the Creative Commons Attribution 2.0 International License (https://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Keywords

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

BMC Chemistry

ISSN: 2661-801X

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