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 |

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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