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Introductory video to TIKANIS® PottersWheel.

General design and workflow

PottersWheel Model Designer





PottersWheel is a MATLAB toolbox for mathematical modeling of time-dependent dynamical systems that can be expressed as chemical reaction networks or ordinary differential equations (ODEs). It allows to automatically calibrate model parameters by fitting the model to experimental measurements. CPU-intensive functions are written or – in case of model dependent functions – dynamically generated in C. Modeling can be done interactively using graphical user interfaces or based on MATLAB scripts using the PottersWheel function library. The software intends to support the work of a mathematical modeler as a real potter's wheel eases the modeling of pottery.

Its fast numerical solver enables users to investigate the dynamic properties of their model by changing model parameters and the shape of the driving input functions interactively with a set of sliding parameter bars. When fitting experimental data, users can apply external driving input function like pulsed or continuous stimulations to estimate kinetic parameters. This increases the power to distinguish competing model hypotheses.

Several optimization algorithms are supported including line search, trust-region, genetic algorithm and simulated annealing. Rule-based modeling simplfies the creation and maintenance of models with combinatorial complexity. A functionality-rich application programming interface (API) allows users to integrate PottersWheel into other MATLAB programs. PottersWheel comes with a macro programming environment to automate and document any modeling work.

PottersWheel features:

  • Reaction network or ordinary differential equation (ODE) based modeling
  • Multi-experimental fitting
  • Fast numerical optimization based on FORTRAN integrators and C MEX ODE files
  • Accessible via graphical user interface, command lines and scripts
  • Determines parameter identifiability and confidence intervals
  • Imports and Exports SBML (Systems Biology Marked-up Language) models to enhance sharing facility
  • Supports biochemical network modeling
  • Applicable for arbitrary ODE based modeling


For a downloadable demo version of PottersWheel, visit