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.

AuthorRoberto Bertolusso and Marek Kimmel
Date of publication2014-03-04 21:55:07
MaintainerRoberto Bertolusso <rbertolusso@rice.edu>
LicenseGPL (>= 2)
Version1.2.0

View on CRAN

Functions

atr Man page
bioPN-package Man page
GibsonBruck Man page
GillespieDirectCR Man page
GillespieDirectGB Man page
GillespieOptimDirect Man page
HaseltineRawlings Man page
init Man page
load.cfn Man page
PartitionedLeaping Man page
RungeKuttaDormandPrince45 Man page
unload.cfns Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.