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bioPN  

Simulation of deterministic and stochastic biochemical reaction networks using Petri Nets
View on CRAN: Click here


Download and install bioPN package within the R console
Install from CRAN:
install.packages("bioPN")

Install from Github:
library("remotes")
install_github("cran/bioPN")

Install by package version:
library("remotes")
install_version("bioPN", "1.2.0")



Attach the package and use:
library("bioPN")
Maintained by
Roberto Bertolusso
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2014-03-04
Latest Update:
Description:
bioPN is a package suited to perform simulation of deterministic and stochastic systems of biochemical reactionnetworks.Models are defined using a subset of Petri Nets, in a way that is close at how chemical reactionsare defined.For deterministic solutions, bioPN creates the associated system of differential equations "on the fly", andsolves 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.
How to cite:
Roberto Bertolusso (2014). bioPN: Simulation of deterministic and stochastic biochemical reaction networks using Petri Nets. R package version 1.2.0, https://cran.r-project.org/web/packages/bioPN. Accessed 25 Jun. 2026.
Previous versions and publish date:
1.2.0 (2014-03-04 21:55)
Other packages that cited bioPN R package
View bioPN citation profile
Other R packages that bioPN depends, imports, suggests or enhances
Complete documentation for bioPN
Functions, R codes and Examples using the bioPN R package
Some associated functions: bioPN-package . helper . simulation . 
Some associated R codes: GibsonBruck.R . GillespieDirectCR.R . GillespieDirectGB.R . GillespieOptimDirect.R . HaseltineRawlings.R . PartitionedLeaping.R . RungeKuttaDormandPrince45.R . helper.R .  Full bioPN package functions and examples
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