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sbioPN  

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


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

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

Install by package version:
library("remotes")
install_version("sbioPN", "1.1.0")



Attach the package and use:
library("sbioPN")
Maintained by
Roberto Bertolusso
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2014-03-15
Latest Update: 2024-01-12
Description:
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.
How to cite:
Roberto Bertolusso (2014). sbioPN: sbioPN: Simulation of deterministic and stochastic spatial biochemical reaction networks using Petri Nets. R package version 1.1.0, https://cran.r-project.org/web/packages/sbioPN. Accessed 28 Mar. 2025.
Previous versions and publish date:
1.1.0 (2014-03-15 18:37)
Other packages that cited sbioPN R package
View sbioPN citation profile
Other R packages that sbioPN depends, imports, suggests or enhances
Functions, R codes and Examples using the sbioPN R package
Some associated functions: helper . sbioPN-package . simulation . 
Some associated R codes: helper.R . sGillespieDirectCR.R . sGillespieOptimDirect.R . sHaseltineRawlings.R . sRungeKuttaDormandPrince45.R .  Full sbioPN package functions and examples
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