Volume 3 Supplement 1

4th German Conference on Chemoinformatics: 22. CIC-Workshop

Open Access

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

  • T Kuhn1, 2,
  • A Zielesny2 and
  • C Steinbeck3
Chemistry Central Journal20093(Suppl 1):P42

https://doi.org/10.1186/1752-153X-3-S1-P42

Published: 05 June 2009

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. Additionally an implementation of the ART2a [5] algorithm is added as worker and could be used for cluster purposes. Worker which analyse and compare the cluster results are also implemented. Pgchem::Tigress [6] a chemoinformatic cartridge for a PostgresSQL database is used to allow the handling of large datasets. Therefore a number of worker for adding, selection and searching molecules from and on the database are added.

Authors’ Affiliations

(1)
Cologne University Bioinformatics Center (CUBIC)
(2)
University of Applied Sciences of Gelsenkirchen, Institute for Bioinformatics and Chemoinformatics
(3)
European Bioinformatics Institute (EBI)

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.View ArticleGoogle 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.View ArticleGoogle Scholar
  3. Spjuth O, Helmus T, Willighagen EL, Kuhn S, Eklund M, et al: Bioclipse: An open rich client workbench for chemo-and bioinformatics.Google Scholar
  4. Witten IH, Frank E: Data Mining: Practical machine learning tools and techniques. 2005, Morgen Kaufmann, San Francisco, 2Google Scholar
  5. Carpenter GA, Grossberg S, Rosen DB: Neural Networks. 1991, 4: 493-10.1016/0893-6080(91)90045-7.View ArticleGoogle Scholar
  6. Schmid EG: [http://pgfoundry.org/projects/pgchem/]

Copyright

© Kuhn et al; licensee BioMed Central Ltd. 2009

This article is published under license to BioMed Central Ltd.