sbioPN: sbioPN: Simulation of deterministic and stochastic spatial biochemical reaction networks using Petri Nets. sbioPN is a package suited to perform simulation of deterministic and stochastic systems of biochemical reaction networks with spatial effects. Models are defined using a subset of Petri Nets, in a way that is close at how chemical reactions are defined. For deterministic solutions, sbioPN creates the associated system of differential equations ”on the fly”, and solves it with a Runge Kutta Dormand Prince 45 explicit algorithm. For stochastic solutions, sbioPN offers two variants of Gillespie algorithm, or SSA. For hybrid deterministic/stochastic, it employs the Haseltine and Rawlings algorithm, that partitions the system in fast and slow reactions. sbioPN algorithms are developed in C to achieve adequate performance.
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References in zbMATH (referenced in 3 articles , 1 standard article )
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- Bertolusso, Roberto; Kimmel, Marek: Spatial and stochastic effects in a model of viral infection (2012)