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)


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

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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