Uses of Class
de.bioforscher.singa.simulation.modules.model.Simulation

Packages that use Simulation

Package	Description
de.bioforscher.singa.simulation.modules.model
de.bioforscher.singa.simulation.modules.reactions.implementations
de.bioforscher.singa.simulation.modules.reactions.model
de.bioforscher.singa.simulation.modules.transport

Uses of Simulation in de.bioforscher.singa.simulation.modules.model

Methods in de.bioforscher.singa.simulation.modules.model that return Simulation

Modifier and Type	Method and Description
static Simulation	SimulationExamples.createCompartmentTestEnvironment()
static Simulation	SimulationExamples.createDecompositionReactionExample() This simulation simulates the thermal decomposition of dinitrogen pentaoxide.
static Simulation	SimulationExamples.createDiffusionAndMembraneTransportExample()
static Simulation	SimulationExamples.createDiffusionModuleExample(int numberOfNodes, javax.measure.Quantity<javax.measure.quantity.Time> timeStep) This simulation simulates a diffusion of small molecules in a rectangular gird graph.
static Simulation	SimulationExamples.createEquilibriumReactionExample() This simulation simulates a equilibrium reaction.
static Simulation	SimulationExamples.createIodineMultiReactionExample() This simulation simulates a multiple reactions involving iodine.
static Simulation	SimulationExamples.createMichaelisMentenReactionExample() This simulation simulates a MichaelisMentenReaction, where D-Fructose 1-phosphate is convertet to glycerone phosphate and D-glyceraldehyde using fructose bisphosphate aldolase.
static Simulation	SimulationExamples.createPassiveMembraneTransportExample()
static Simulation	SimulationExamples.createSimulationFromSBML()
static Simulation	SimulationExamples.createSynthesisReactionExample() This simulation simulates the synthesis of 1,3,5-octatriene (C8H12) from Buta-1,3-diene (C4H6).
Simulation	AbstractSectionSpecificModule.getSimulation()
Simulation	AbstractNeighbourIndependentModule.getSimulation()

Methods in de.bioforscher.singa.simulation.modules.model with parameters of type Simulation

Modifier and Type	Method and Description
void	AbstractSectionSpecificModule.setSimulation(Simulation simulation)
void	AbstractNeighbourIndependentModule.setSimulation(Simulation simulation)

Constructors in de.bioforscher.singa.simulation.modules.model with parameters of type Simulation

Constructor and Description
AbstractNeighbourDependentModule(Simulation simulation)
AbstractNeighbourIndependentModule(Simulation simulation)
AbstractSectionSpecificModule(Simulation simulation)
TimeStepHarmonizer(Simulation simulation, javax.measure.Quantity<javax.measure.quantity.Time> initialTimeStep)

Uses of Simulation in de.bioforscher.singa.simulation.modules.reactions.implementations

Constructors in de.bioforscher.singa.simulation.modules.reactions.implementations with parameters of type Simulation

Constructor and Description
DynamicReaction(Simulation simulation, DynamicKineticLaw kineticLaw)
EquilibriumReaction(Simulation simulation, javax.measure.Quantity<javax.measure.quantity.Frequency> forwardsRateConstant, javax.measure.Quantity<javax.measure.quantity.Frequency> backwardsRateConstant)
MichaelisMentenReaction(Simulation simulation, Enzyme enzyme)
NthOrderReaction(Simulation simulation, javax.measure.Quantity<javax.measure.quantity.Frequency> rateConstant)

Uses of Simulation in de.bioforscher.singa.simulation.modules.reactions.model

Constructors in de.bioforscher.singa.simulation.modules.reactions.model with parameters of type Simulation

Constructor and Description
Reaction(Simulation simulation)

Uses of Simulation in de.bioforscher.singa.simulation.modules.transport

Constructors in de.bioforscher.singa.simulation.modules.transport with parameters of type Simulation

Constructor and Description
FreeDiffusion(Simulation simulation)
PassiveMembraneTransport(Simulation simulation)