Packages

fern
fern.analysis	Provides classes and algorithms for analysing networks like ShortestPath, AutocatalyticDetection.
fern.benchmark	Provides classes for benchmarking simulations (time benchmarks, histogram distance calculation).
fern.cellDesigner
fern.cellDesigner.ui
fern.cytoscape	Provides the classes for the cytoscape plugin.
fern.cytoscape.ui
fern.example	Contains examples and demonstrations of the framework.
fern.network	Provides general classes and interfaces for storing network data.
fern.network.creation	Provides classes for the evolution of networks.
fern.network.fernml	Provides the classes for parsing and using FernML based networks.
fern.network.modification	Provides classes for modifications of networks.
fern.network.sbml	Provides the classes for parsing and using sbml based networks.
fern.simulation	Provides algorithms for simulating reaction network as well as methods for observer certain aspects of a simulation.
fern.simulation.algorithm	Provides algorithms for stochastic simultion of reaction networks.
fern.simulation.controller	Provides classes to control the simulations.
fern.simulation.observer	Provides classes to observe certain aspects of simulations.
fern.tools	Provides common used tools.
fern.tools.functions	Provides common function delegates and implementations.
fern.tools.gnuplot	Provides classes to use gnuplot from java.