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 |
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