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.
Version: |
1.2.0 |
Published: |
2014-03-04 |
DOI: |
10.32614/CRAN.package.bioPN |
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: |
bioPN results [issues need fixing before 2024-09-23] |
Documentation:
Downloads:
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