# 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.

- 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

## 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 |