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Mathematical Modeling of Biochemical Systems with PottersWheel

  • Thomas MaiwaldEmail author
  • Oliver Eberhardt
  • Julie Blumberg
Part of the Methods in Molecular Biology book series (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.

Key words

Computer Simulation Systems Biology Computational Biology Biological models Signal Transduction Methods Software Modeling framework Matlab toolbox Parameter estimation Multi-experiment fitting ODE 

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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Thomas Maiwald
    • 1
    • 2
    Email author
  • Oliver Eberhardt
    • 2
  • Julie Blumberg
    • 2
  1. 1.Freiburg Center for Systems BiologyUniversity of FreiburgFreiburgGermany
  2. 2.Scientific SoftwareTIKANIS SolutionsFreiburgGermany

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