title: Computational modeling of biochemical networks using COPASI.
abstract: 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.
authors.affiliation: Manchester Centre for Integrative Systems Biology, University of Manchester, UK.
authors.forename: Pedro
authors.initials: P
authors.lastname: Mendes
authors.forename: Stefan
authors.initials: S
authors.lastname: Hoops
authors.forename: Sven
authors.initials: S
authors.lastname: Sahle
authors.forename: Ralph
authors.initials: R
authors.lastname: Gauges
authors.forename: Joseph
authors.initials: J
authors.lastname: Dada
authors.forename: Ursula
authors.initials: U
authors.lastname: Kummer
mesh_terms: D000465:Algorithms; D000818:Animals; D003198:Computer Simulation; D006801:Humans; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D012984:Software; D049490:Systems Biology / Q000379:methods*