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.
Package details |
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Author | Roberto Bertolusso and Marek Kimmel |
Maintainer | Roberto Bertolusso <rbertolusso@rice.edu> |
License | GPL (>= 2) |
Version | 1.2.0 |
Package repository | View on CRAN |
Installation |
Install the latest version of this package by entering the following in R:
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