bioPN: Simulation of deterministic and stochastic biochemical reaction networks using Petri Nets

bioPN is a package suited to perform simulation of deterministic and stochastic systems of biochemical reaction networks. Models are defined using a subset of Petri Nets, in a way that is close at how chemical reactions are defined. For deterministic solutions, bioPN 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, bioPN offers 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. bioPN algorithms are developed in C to achieve adequate performance.

Package details

AuthorRoberto Bertolusso and Marek Kimmel
MaintainerRoberto Bertolusso <[email protected]>
LicenseGPL (>= 2)
Package repositoryView on CRAN
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bioPN documentation built on May 29, 2017, 5:57 p.m.