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Systems Biology

Volume 500 of the series Methods in Molecular Biology pp 17-59

Date:

Computational Modeling of Biochemical Networks Using COPASI

  • Pedro MendesAffiliated withSchool of Computer Science and Manchester Centre for Integrative Systems Biology, University of Manchester Email author 
  • , Stefan Hoops
  • , Sven Sahle
  • , Ralph Gauges
  • , Joseph Dada
  • , Ursula Kummer

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Summary

Computational modeling and simulation of biochemical networks is at the core of systems biology and this includes many types of analyses that can aid understanding of how these systems work. COPASI is a generic software package for modeling and simulation of biochemical networks which provides many of these analyses in convenient ways that do not require the user to program or to have deep knowledge of the numerical algorithms. Here we provide a description of how these modeling techniques can be applied to biochemical models using COPASI. The focus is both on practical aspects of software usage as well as on the utility of these analyses in aiding biological understanding. Practical examples are described for steady-state and time-course simulations, stoichiometric analyses, parameter scanning, sensitivity analysis (including metabolic control analysis), global optimization, parameter estimation, and stochastic simulation. The examples used are all published models that are available in the BioModels database in SBML format.

Keywords

Simulation Modeling Systems biology Optimization Stochastic simulation Sensitivity analysis Parameter estimation SBML Stoichiometric analysis