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.
Package details 


Author  Roberto Bertolusso and Marek Kimmel 
Date of publication  20140315 18:37:54 
Maintainer  Roberto Bertolusso <rbertolusso@rice.edu> 
License  GPL (>= 2) 
Version  1.1.0 
Package repository  View on CRAN 
Installation 
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