Documentation

 

The PottersWheel introduction (PDF, 2,8MB) provides an overview of the underlying concept and functionalities of the software.

The videos section gives you a quick impression of how to use PottersWheel.

The tutorials First steps, Fitting, and in the tutorials section exemplify step-by-step how to simulate synthetic data or to fit experimental measurements.

The list of important functions is a good starting point in order to use PottersWheel from command line or within own Matlab scripts. The complete function reference contains the same information as when typing help functionName in the Matlab command window. The terminology section may serve as a reminder to the basic methodology.

Example models and data sets are included in the PottersWheel toolbox. Use either the menu Model | Add model from library and Data | Add data from library, the magnifying glass to search the model library, or open the ModelLibrary and DataLibrary folders in the toolbox folder directly.

The old documentation of version 1.4 is still available. The implemented concepts are described in

Dynamical Modeling and Multi-Experiment Fitting with PottersWheel
T. Maiwald and J. Timmer
Bioinformatics 2008, 24(18):2037-2043

Data-based identifiability analysis of nonlinear dynamical models
S. Hengl, C. Kreutz, J. Timmer, T Maiwald
Bioinformatics 2007, 23, 2612-2618

Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood
A. Raue, C. Kreutz, T. Maiwald, J. Bachmann, M. Schilling, U. Klingm├╝ller, J. Timmer
Bioinformatics 2009, 25(15):1923-1929