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.

Author
Roberto Bertolusso and Marek Kimmel
Date of publication
2014-03-04 21:55:07
Maintainer
Roberto Bertolusso <rbertolusso@rice.edu>
License
GPL (>= 2)
Version
1.2.0

View on CRAN

Man pages

bioPN-package
Simulation of deterministic and stochastic biochemical...
helper
Helper functions for model definition
simulation
Simulation of a biochemical system

Files in this package

bioPN
bioPN/COPYING
bioPN/inst
bioPN/inst/COPYRIGHTS
bioPN/src
bioPN/src/helper.h
bioPN/src/GillespieOptimDirect.c
bioPN/src/GibsonBruck.c
bioPN/src/helper.c
bioPN/src/quicksort.c
bioPN/src/prdgrm.c
bioPN/src/GillespieDirectGB.c
bioPN/src/PartitionedLeaping.c
bioPN/src/quicksort.h
bioPN/src/mean_sd.c
bioPN/src/GillespieDirectCR.c
bioPN/src/HaseltineRawlings.c
bioPN/NAMESPACE
bioPN/R
bioPN/R/GillespieDirectGB.R
bioPN/R/PartitionedLeaping.R
bioPN/R/GillespieOptimDirect.R
bioPN/R/GillespieDirectCR.R
bioPN/R/GibsonBruck.R
bioPN/R/helper.R
bioPN/R/HaseltineRawlings.R
bioPN/R/RungeKuttaDormandPrince45.R
bioPN/MD5
bioPN/DESCRIPTION
bioPN/man
bioPN/man/simulation.Rd
bioPN/man/bioPN-package.Rd
bioPN/man/helper.Rd