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.

Version: 1.1.0
Published: 2014-03-15
Author: Roberto Bertolusso and Marek Kimmel
Maintainer: Roberto Bertolusso <rbertolusso at rice.edu>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
Copyright: see file COPYRIGHTS
NeedsCompilation: yes
CRAN checks: sbioPN results

Downloads:

Reference manual: sbioPN.pdf
Package source: sbioPN_1.1.0.tar.gz
Windows binaries: r-devel: sbioPN_1.1.0.zip, r-release: sbioPN_1.1.0.zip, r-oldrel: sbioPN_1.1.0.zip
OS X El Capitan binaries: r-release: sbioPN_1.1.0.tgz
OS X Mavericks binaries: r-oldrel: sbioPN_1.1.0.tgz

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