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 |
| 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 |
| Reference manual: | bioPN.pdf |
| Package source: | bioPN_1.2.0.tar.gz |
| Windows binaries: | r-devel: bioPN_1.2.0.zip, r-release: bioPN_1.2.0.zip, r-oldrel: bioPN_1.2.0.zip |
| macOS binaries: | r-release: bioPN_1.2.0.tgz, r-oldrel: bioPN_1.2.0.tgz |
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