swMATH ID: 11725
Software Authors: Roberto Bertolusso; Marek Kimmel
Description: 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.
Homepage: http://cran.r-project.org/web/packages/sbioPN/index.html
Source Code:  https://github.com/cran/sbioPN
Dependencies: R
Related Software: SPPARKS
Cited in: 6 Publications

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