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Bioinformatics Advance Access originally published online on July 9, 2008
Bioinformatics 2008 24(18):2037-2043; doi:10.1093/bioinformatics/btn350
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Dynamical modeling and multi-experiment fitting with PottersWheel

Thomas Maiwald 1,2,* and Jens Timmer 1,2

1Freiburg Center for Data Analysis and Modeling, Freiburg University, Eckerstr. 1, 79104 Freiburg and 2Institute of Physics, Freiburg University, Hermann Herder Str. 3, 79104 Freiburg, Germany

*To whom correspondence should be addressed


  Abstract

Motivation: Modelers in Systems Biology need a flexible framework that allows them to easily create new dynamic models, investigate their properties and fit several experimental datasets simultaneously. Multi-experiment-fitting is a powerful approach to estimate parameter values, to check the validity of a given model, and to discriminate competing model hypotheses. It requires high-performance integration of ordinary differential equations and robust optimization.

Results: We here present the comprehensive modeling framework Potters-Wheel (PW) including novel functionalities to satisfy these requirements with strong emphasis on the inverse problem, i.e. data-based modeling of partially observed and noisy systems like signal transduction pathways and metabolic networks. PW is designed as a MATLAB toolbox and includes numerous user interfaces. Deterministic and stochastic optimization routines are combined by fitting in logarithmic parameter space allowing for robust parameter calibration. Model investigation includes statistical tests for model-data-compliance, model discrimination, identifiability analysis and calculation of Hessian- and Monte-Carlo-based parameter confidence limits. A rich application programming interface is available for customization within own MATLAB code. Within an extensive performance analysis, we identified and significantly improved an integrator–optimizer pair which decreases the fitting duration for a realistic benchmark model by a factor over 3000 compared to MATLAB with optimization toolbox.

Availability: PottersWheel is freely available for academic usage at http://www.PottersWheel.de/. The website contains a detailed documentation and introductory videos. The program has been intensively used since 2005 on Windows, Linux and Macintosh computers and does not require special MATLAB toolboxes.

Contact: maiwald{at}fdm.uni-freiburg.de

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Olga Troyanskaya

Received on February 7, 2008; revised on June 10, 2008; accepted on July 8, 2008

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