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sbioPN

swMATH ID: 11725
Software Authors: Roberto Bertolusso; Marek Kimmel
Description: sbioPN: 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.
Homepage: http://cran.r-project.org/web/packages/sbioPN/index.html
Source Code:  https://github.com/cran/sbioPN
Dependencies: R
Related Software: SPPARKS
Cited in: 6 Publications

Standard Articles

1 Publication describing the Software, including 1 Publication in zbMATH Year
Spatial and stochastic effects in a model of viral infection. Zbl 1306.92057
Bertolusso, Roberto; Kimmel, Marek
2012
all top 5

Cited by 14 Authors

2 Bertolusso, Roberto
2 Kimmel, Marek
1 Bocharov, Gennady A.
1 Du, Yanfei
1 Foo, Jasmine
1 Härting, Steffen
1 Karch, Grzegorz
1 Leder, Kevin
1 Marciniak-Czochra, Anna K.
1 Ryser, Marc Daniel
1 Suzuki, Kanako
1 Tasevich, Alla L’vovna
1 Volpert, Vitaly A.
1 Wei, Junjie
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Cited in 6 Serials

1 Nonlinearity
1 Computational Mathematics and Mathematical Physics
1 International Journal of Bifurcation and Chaos in Applied Sciences and Engineering
1 Fundamenta Informaticae
1 Mathematical Modelling of Natural Phenomena
1 Journal of Theoretical Biology

Cited in 3 Fields

5 Biology and other natural sciences (92-XX)
4 Partial differential equations (35-XX)
1 Ordinary differential equations (34-XX)

Citations by Year