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Packages that use fern.network | |
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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.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.tools | Provides common used tools. |
Classes in fern.network used by fern.analysis | |
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Network
The central interface of the whole framework. |
Classes in fern.network used by fern.benchmark | |
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Network
The central interface of the whole framework. |
Classes in fern.network used by fern.cellDesigner | |
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AbstractNetworkImpl
Base implementation for the Network interface. |
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AmountManager
The AmountManager is one of the most important connections between a
Network and a Simulator . |
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ComplexDependenciesPropensityCalculator
In a SBML network, the propensities of reaction are calculated by using the kineticLaw tag, which contains a MathML expression. |
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Network
The central interface of the whole framework. |
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PropensityCalculator
A PropensityCalculator is the way, a Network tells a Simulator
how to calculate propensities for the reactions. |
Classes in fern.network used by fern.cellDesigner.ui | |
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Network
The central interface of the whole framework. |
Classes in fern.network used by fern.cytoscape | |
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AbstractNetworkImpl
Base implementation for the Network interface. |
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AnnotationManager
AnnotationManager objects are the places, where static (or quasi-static) properties of a network are stored. |
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Network
The central interface of the whole framework. |
Classes in fern.network used by fern.example | |
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FeatureNotSupportedException
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Classes in fern.network used by fern.network | |
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AbstractKineticConstantPropensityCalculator
Base implementation of a PropensityCalculator . |
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AmountManager
The AmountManager is one of the most important connections between a
Network and a Simulator . |
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AnnotationManager
AnnotationManager objects are the places, where static (or quasi-static) properties of a network are stored. |
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FeatureNotSupportedException
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KineticConstantPropensityCalculator
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Network
The central interface of the whole framework. |
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PartialDerivativePropensityCalculator
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PropensityCalculator
A PropensityCalculator is the way, a Network tells a Simulator
how to calculate propensities for the reactions. |
Classes in fern.network used by fern.network.creation | |
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AbstractNetworkImpl
Base implementation for the Network interface. |
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Network
The central interface of the whole framework. |
|
PropensityCalculator
A PropensityCalculator is the way, a Network tells a Simulator
how to calculate propensities for the reactions. |
Classes in fern.network used by fern.network.fernml | |
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AbstractNetworkImpl
Base implementation for the Network interface. |
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AnnotationManager
AnnotationManager objects are the places, where static (or quasi-static) properties of a network are stored. |
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ArrayKineticConstantPropensityCalculator
Implementation of an AbstractKineticConstantPropensityCalculator which uses
an array to store the constants for each reaction. |
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Network
The central interface of the whole framework. |
Classes in fern.network used by fern.network.modification | |
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AmountManager
The AmountManager is one of the most important connections between a
Network and a Simulator . |
|
AnnotationManager
AnnotationManager objects are the places, where static (or quasi-static) properties of a network are stored. |
|
Network
The central interface of the whole framework. |
|
PropensityCalculator
A PropensityCalculator is the way, a Network tells a Simulator
how to calculate propensities for the reactions. |
Classes in fern.network used by fern.network.sbml | |
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AbstractNetworkImpl
Base implementation for the Network interface. |
|
AmountManager
The AmountManager is one of the most important connections between a
Network and a Simulator . |
|
ComplexDependenciesPropensityCalculator
In a SBML network, the propensities of reaction are calculated by using the kineticLaw tag, which contains a MathML expression. |
|
FeatureNotSupportedException
|
|
Network
The central interface of the whole framework. |
|
PropensityCalculator
A PropensityCalculator is the way, a Network tells a Simulator
how to calculate propensities for the reactions. |
Classes in fern.network used by fern.simulation | |
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Network
The central interface of the whole framework. |
|
PropensityCalculator
A PropensityCalculator is the way, a Network tells a Simulator
how to calculate propensities for the reactions. |
Classes in fern.network used by fern.simulation.algorithm | |
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Network
The central interface of the whole framework. |
Classes in fern.network used by fern.tools | |
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FeatureNotSupportedException
|
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Network
The central interface of the whole framework. |
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