Computational Modeling of Biochemical Networks Using COPASI
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.
KeywordsSimulation Modeling Systems biology Optimization Stochastic simulation Sensitivity analysis Parameter estimation SBML Stoichiometric analysis
We thank the users of COPASI whose feedback on the software is crucial for its continued improvement. We also thank all developers who have actively contributed to COPASI. COPASI development is supported financially by generous funding from the US National Institute for General Medical Sciences (GM080219), the Virginia Bioinformatics Institute, the Klaus Tschira Foundation, the German Ministry of Education and Research (BMBF), and the UK BBSRC/EPSRC through The Manchester Centre for Integrative Systems Biology.
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