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

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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.

Author
Roberto Bertolusso and Marek Kimmel
Date of publication
2014-03-15 18:37:54
Maintainer
Roberto Bertolusso <rbertolusso@rice.edu>
License
GPL (>= 2)
Version
1.1.0

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Man pages

helper
Helper functions for model definition
sbioPN-package
Simulation of deterministic and stochastic biochemical...
simulation
Simulation of a biochemical system with spatial effects

Files in this package

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