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:
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)
| # Install 'bioPN' in R: |
| install.packages('bioPN', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 11 years agofrom:0e8de933c4. Checks:OK: 1 NOTE: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 24 2024 |
| R-4.5-linux-x86_64 | NOTE | Oct 24 2024 |
Exports:atrGibsonBruckGillespieDirectCRGillespieDirectGBGillespieOptimDirectHaseltineRawlingsinitload.cfnPartitionedLeapingRungeKuttaDormandPrince45unload.cfns
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Simulation of deterministic and stochastic biochemical reaction networks using Petri Nets | bioPN-package |
| Simulation of a biochemical system | GibsonBruck GillespieDirectCR GillespieDirectGB GillespieOptimDirect HaseltineRawlings PartitionedLeaping RungeKuttaDormandPrince45 |
| Helper functions for model definition | atr init load.cfn unload.cfns |