Package fern.example

Class Summary

Class	Description
AutocatalyticNetworkExample	Here, the evolution of a reaction network as proposed by [1] is performed.
CellGrowthObserver	Does not observe anything, but it controls the reaction networks cell.
CompositionRejectionStressTest
DecayingDimerizingHistogramDistances	Demonstration of performance and accuracy differences of the different simulation algorithms.
DecayingDimerizingInteractive	Demonstration of performance and accuracy differences of the different simulation algorithms.
DecayingDimerizingPlots	Deprecated
Dsmts	Perform a series of tests (refer to http://www.calibayes.ncl.ac.uk/Resources/dsmts).
ExamplePath	Determine the path to the example network files.
HistogramDistanceTestSet	Encapsulate test sets for histogram distance calculations.
IrreversibleIsomerization	Uses the Irreversible-isomerization model to show effects of different choices for epsilon.
LacYComplete	The LacZ/LacY model of procaryotic gene expression proposed by [1] is simulated.
LacYHistogramDistances	The LacZ/LacY model of procaryotic gene expression proposed by [1] is simulated.
LacZ	The LacZ/LacY model of procaryotic gene expression proposed by [1] is simulated.
Mapk	The most basic example uses the famous enzyme kinetics equation by Michaelis and Menten S + E ⇌ ES → P to introduce fundamental loading and repeated simulation of reaction networks.
MapkBenchmark	Use the signal transduction pathway network of the epidermal growth factor proposed by [1] to introduce the benchmark system.
MichaelisMentenKinetic	The most basic example uses the famous enzyme kinetics equation by Michaelis and Menten S + E ⇌ ES → P to introduce fundamental loading and repeated simulation of reaction networks.
SBMLMathTreeTest