Package: bioPN 1.2.0

Roberto Bertolusso

bioPN: Simulation of deterministic and stochastic biochemical reaction networks using Petri Nets

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.

Authors:Roberto Bertolusso and Marek Kimmel

bioPN_1.2.0.tar.gz
bioPN_1.2.0.tar.gz(r-4.5-noble)bioPN_1.2.0.tar.gz(r-4.4-noble)
bioPN_1.2.0.tgz(r-4.4-emscripten)bioPN_1.2.0.tgz(r-4.3-emscripten)
bioPN.pdf |bioPN.html✨
bioPN/json (API)

Peer review:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

11 exports 1 stars 0.36 score 0 dependencies 1 mentions 2 scripts 176 downloads

Last updated 11 years agofrom:0e8de933c4. Checks:OK: 1 NOTE: 1. Indexed: yes.

Exports:atrGibsonBruckGillespieDirectCRGillespieDirectGBGillespieOptimDirectHaseltineRawlingsinitload.cfnPartitionedLeapingRungeKuttaDormandPrince45unload.cfns

Dependencies: