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Computational Modeling of Signaling Networks pp 119–138Cite as

Mathematical Modeling of Biochemical Systems with PottersWheel

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 880))

Abstract

The program PottersWheel has been developed to provide an intuitive and yet powerful framework for data-based modeling of dynamical systems like biochemical reaction networks. Its key functionality is multi-experiment fitting, where several experimental data sets from different laboratory conditions are fitted simultaneously in order to improve the estimation of unknown model parameters, to check the validity of a given model, and to discriminate competing model hypotheses. New experiments can be designed interactively. Models are either created text-based or using a visual model designer. Dynamically generated and compiled C files provide fast simulation and fitting procedures. Each function can either be accessed using a graphical user interface or via command line, allowing for batch processing within custom Matlab scripts. PottersWheel is designed as a Matlab toolbox, comprises 250,000 lines of Matlab and C code, and is freely available for academic usage at www.potterswheel.de.

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Author information

Authors and Affiliations

  1. Freiburg Center for Systems Biology, University of Freiburg, Freiburg, Germany

    Thomas Maiwald

  2. Scientific Software, TIKANIS Solutions, Freiburg, Germany

    Thomas Maiwald, Oliver Eberhardt & Julie Blumberg

Authors
  1. Thomas Maiwald
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  2. Oliver Eberhardt
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  3. Julie Blumberg
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Corresponding author

Correspondence to Thomas Maiwald .

Editor information

Editors and Affiliations

  1. Dept. Chemistry & Biochemistry, University of Colorado, Boulder, Boulder, 80309-0215, Colorado, USA

    Xuedong Liu

  2. Dept. Physics, University of Colorado, Boulder, Boulder, 80309, Colorado, USA

    Meredith D. Betterton

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© 2012 Springer Science+Business Media, LLC

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Maiwald, T., Eberhardt, O., Blumberg, J. (2012). Mathematical Modeling of Biochemical Systems with PottersWheel. In: Liu, X., Betterton, M. (eds) Computational Modeling of Signaling Networks. Methods in Molecular Biology, vol 880. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-833-7_8

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  • DOI: https://doi.org/10.1007/978-1-61779-833-7_8

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-61779-832-0

  • Online ISBN: 978-1-61779-833-7

  • eBook Packages: Springer Protocols

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