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.

AuthorRoberto Bertolusso and Marek Kimmel
Date of publication2014-03-15 18:37:54
MaintainerRoberto Bertolusso <rbertolusso@rice.edu>
LicenseGPL (>= 2)
Version1.1.0

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Files

sbioPN
sbioPN/COPYING
sbioPN/inst
sbioPN/inst/COPYRIGHTS
sbioPN/src
sbioPN/src/sGillespieDirectCR.c
sbioPN/src/helper.h
sbioPN/src/helper.c
sbioPN/src/sHaseltineRawlings.c
sbioPN/src/sGillespieOptimDirect.c
sbioPN/src/quicksort.c
sbioPN/src/quicksort.h
sbioPN/NAMESPACE
sbioPN/R
sbioPN/R/sRungeKuttaDormandPrince45.R sbioPN/R/sGillespieDirectCR.R sbioPN/R/sHaseltineRawlings.R sbioPN/R/helper.R sbioPN/R/sGillespieOptimDirect.R
sbioPN/MD5
sbioPN/DESCRIPTION
sbioPN/man
sbioPN/man/simulation.Rd sbioPN/man/helper.Rd sbioPN/man/sbioPN-package.Rd

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