An Advanced Environment for Hybrid Modeling of Biological Systems Based on Modelica

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doi doi:10.2390/biecoll-jib-2011-152
submission July 15, 2010
last revision December 21, 2010
published January 20, 2011
NCBI PubMed PubMed ID 21248370

Sabrina Pross and Bernhard Bachmann

Correspondence should be addressed to:
Sabrina Pross
University of Applied Sciences Bielefeld, Am Stadtholz 24, 33609 Bielefeld, Germany
ed.dlefeleib-hf@nullssorp.anirbas


Abstract

Biological systems are often very complex so that an appropriate formalism is needed for modeling their behavior. Hybrid Petri Nets, consisting of time-discrete Petri Net elements as well as continuous ones, have proven to be ideal for this task. Therefore, a new Petri Net library was implemented based on the object-oriented modeling language Modelica which allows the modeling of discrete, stochastic and continuous Petri Net elements by differential, algebraic and discrete equations. An appropriate Modelica-tool performs the hybrid simulation with discrete events and the solution of continuous differential equations. A special sub-library contains so-called wrappers for specific reactions to simplify the modeling process. The Modelica-models can be connected to Simulink-models for parameter optimization, sensitivity analysis and stochastic simulation in Matlab. The present paper illustrates the implementation of the Petri Net component models, their usage within the modeling process and the coupling between the Modelica-tool Dymola and Matlab/Simulink. The application is demonstrated by modeling the metabolism of Chinese Hamster Ovary Cells.

Reference

Sabrina Pross and Bernhard Bachmann. An Advanced Environment for Hybrid Modeling of Biological Systems Based on Modelica. Journal of Integrative Bioinformatics, 8(1):152, 2011. Online Journal: http://journal.imbio.de/index.php?paper_id=152
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