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.
|Author||Roberto Bertolusso and Marek Kimmel|
|Date of publication||2014-03-04 21:55:07|
|Maintainer||Roberto Bertolusso <[email protected]>|
|License||GPL (>= 2)|
|Package repository||View on CRAN|
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