Biosystems Engineering II pp 109-138

Part of the Advances in Biochemical Engineering / Biotechnology book series (ABE, volume 121) | Cite as

Modeling Languages for Biochemical Network Simulation: Reaction vs Equation Based Approaches

Chapter

Abstract

Biochemical network modeling and simulation is an essential task in any systems biology project. The systems biology markup language (SBML) was established as a standardized model exchange language for mechanistic models. A specific strength of SBML is that numerous tools for formulating, processing, simulation and analysis of models are freely available. Interestingly, in the field of multidisciplinary simulation, the problem of model exchange between different simulation tools occurred much earlier. Several general modeling languages like Modelica have been developed in the 1990s. Modelica enables an equation based modular specification of arbitrary hierarchical differential algebraic equation models. Moreover, libraries for special application domains can be rapidly developed. This contribution compares the reaction based approach of SBML with the equation based approach of Modelica and explains the specific strengths of both tools. Several biological examples illustrating essential SBML and Modelica concepts are given. The chosen criteria for tool comparison are flexibility for constraint specification, different modeling flavors, hierarchical, modular and multidisciplinary modeling. Additionally, support for spatially distributed systems, event handling and network analysis features is discussed. As a major result it is shown that the choice of the modeling tool has a strong impact on the expressivity of the specified models but also strongly depends on the requirements of the application context.

Keywords

Biochemical network modeling Modelica Modeling languages Object oriented modeling SBML 

Abbreviations

DAE

differential algebraic equation

PDAE

partial differential algebraic equation

PDE

partial differential equation

SBML

systems biology markup language

XML

extended markup language

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Copyright information

© Springer 2009

Authors and Affiliations

  • Wolfgang Wiechert
    • 1
  • Stephan Noack
    • 1
  • Atya Elsheikh
    • 1
  1. 1.Institut für Biotechnologie 2Forschungszentrum JülichJülichGermany

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