de.bioforscher.singa.simulation.modules.model

Class SimulationExamples

java.lang.Object

de.bioforscher.singa.simulation.modules.model.SimulationExamples

public class SimulationExamples
extends Object

A factory class that can be used to create different examples to test and explore certain aspects to the api.

Author:

cl

Constructor Summary

Constructors

Constructor and Description
SimulationExamples()

Method Summary

Modifier and Type	Method and Description
static Simulation	createCompartmentTestEnvironment()
static Simulation	createDecompositionReactionExample() This simulation simulates the thermal decomposition of dinitrogen pentaoxide.
static Simulation	createDiffusionAndMembraneTransportExample()
static Simulation	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	createEquilibriumReactionExample() This simulation simulates a equilibrium reaction.
static Simulation	createIodineMultiReactionExample() This simulation simulates a multiple reactions involving iodine.
static Simulation	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	createPassiveMembraneTransportExample()
static Simulation	createSimulationFromSBML()
static Simulation	createSynthesisReactionExample() This simulation simulates the synthesis of 1,3,5-octatriene (C8H12) from Buta-1,3-diene (C4H6).

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SimulationExamples

public SimulationExamples()

Method Detail

createDecompositionReactionExample

public static Simulation createDecompositionReactionExample()

This simulation simulates the thermal decomposition of dinitrogen pentaoxide. From: Brauer, G. (2012). Handbook of preparative inorganic chemistry, volume 2. Elsevier. 489–491.

Returns:

The ready to go simulation.

createSynthesisReactionExample

public static Simulation createSynthesisReactionExample()

This simulation simulates the synthesis of 1,3,5-octatriene (C8H12) from Buta-1,3-diene (C4H6).

Returns:

The ready to go simulation.

createEquilibriumReactionExample

public static Simulation createEquilibriumReactionExample()

This simulation simulates a equilibrium reaction.

Returns:

The ready to go simulation.

createMichaelisMentenReactionExample

public static Simulation createMichaelisMentenReactionExample()

This simulation simulates a MichaelisMentenReaction, where D-Fructose 1-phosphate is convertet to glycerone phosphate and D-glyceraldehyde using fructose bisphosphate aldolase. From: Callens, M. et al. (1991). Kinetic properties of fructose bisphosphate aldolase from Trypanosoma brucei compared to aldolase from rabbit muscle and Staphylococcus aureus. Sabio-RK pdbIdentifier: 28851

Returns:

The ready to go simulation.

createDiffusionModuleExample

public static Simulation createDiffusionModuleExample(int numberOfNodes,
                                                      javax.measure.Quantity<javax.measure.quantity.Time> timeStep)

This simulation simulates a diffusion of small molecules in a rectangular gird graph.

Parameters:

numberOfNodes - The number of nodes on one "side" of the rectangle.

timeStep - The size of the time step.

Returns:

The ready to go simulation.

createIodineMultiReactionExample

public static Simulation createIodineMultiReactionExample()

This simulation simulates a multiple reactions involving iodine.

Returns:

The ready to go simulation.

createSimulationFromSBML

public static Simulation createSimulationFromSBML()

createCompartmentTestEnvironment

public static Simulation createCompartmentTestEnvironment()

createPassiveMembraneTransportExample

public static Simulation createPassiveMembraneTransportExample()

createDiffusionAndMembraneTransportExample

public static Simulation createDiffusionAndMembraneTransportExample()