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International Workshop on Data Integration in the Life Sciences

DILS 2009: Data Integration in the Life Sciences pp 182–195Cite as

Design and Architecture of Web Services for Simulation of Biochemical Systems

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Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 5647))

Abstract

Computer simulation of biochemical networks plays a central role in systems biology. While there are several software packages for modeling and simulation of these networks, they are based on graphical user interfaces that operate on the local computer. However, it is now often desirable to operate simulation tasks through a distributed computing framework where data can be gathered from different sources and distinct subtasks operated in different physical computers. In this paper we describe a web services implementation for the COPASI biochemical network simulator (CopasiWS). COPASI provides a range of numerical methods for simulation, optimization and analysis of biochemical reaction networks. Our aim is to allow easy integration of these powerful functionalities with local and remote services to provide a distributed computing platform for the simulation and analysis of biochemical models. One immediate result of this work is that simulation tasks are now available to be used in a platform– and language–independent manner as components of distributed workflows, for example using the Taverna workflow engine. We describe the CopasiWS architecture, key design and implementation issues, and illustrate the range of services available through a web portal interface (CopasiWeb).

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Author information

Authors and Affiliations

  1. School of Computer Science and Manchester Centre for Integrative Systems Biology, The University of Manchester, Manchester Interdisciplinary Biocentre, 131 Princess Street, Manchester, M1 7DN, UK

    Joseph O. Dada & Pedro Mendes

  2. Virginia Bioinformatics Institute, Virginia Tech, Washington Street 0477, Blacksburg, VA, 24060, USA

    Pedro Mendes

Authors
  1. Joseph O. Dada
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  2. Pedro Mendes
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Editor information

Editors and Affiliations

  1. School of Computer Science, University of Manchester, M13 9PL, Manchester, UK

    Norman W. Paton  & Paolo Missier  & 

  2. School of Computer Science, The University of Manchester, Oxford Road, M13 9PL, Manchester, UK

    Cornelia Hedeler

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Dada, J.O., Mendes, P. (2009). Design and Architecture of Web Services for Simulation of Biochemical Systems. In: Paton, N.W., Missier, P., Hedeler, C. (eds) Data Integration in the Life Sciences. DILS 2009. Lecture Notes in Computer Science(), vol 5647. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-02879-3_15

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  • DOI: https://doi.org/10.1007/978-3-642-02879-3_15

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-02878-6

  • Online ISBN: 978-3-642-02879-3

  • eBook Packages: Computer ScienceComputer Science (R0)

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