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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) Cite this article

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

  1. 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.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

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

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

    Google Scholar 

  5. 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.

    Article  CAS  Google Scholar 

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Authors and 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

Authors
  1. Thomas Kuhn
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  2. Achim Zielesny
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  3. Christoph Steinbeck
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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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Kuhn, T., Zielesny, A. & Steinbeck, C. Creating chemo- & bioinformatics workflows, further developments within the CDK-Taverna Project. Chemistry Central Journal 2 (Suppl 1), P27 (2008). https://doi.org/10.1186/1752-153X-2-S1-P27

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  • DOI: https://doi.org/10.1186/1752-153X-2-S1-P27

Keywords

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

BMC Chemistry

ISSN: 2661-801X

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