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java.lang.Objectfern.simulation.Simulator
fern.simulation.algorithm.HybridMaximalTimeStep
public class HybridMaximalTimeStep
This is an modified version of Maximal Time Step Method by Puchalka and Kierzec.
Reactions are divided into slow and fast reaction. The slow ones are fired according
to Gillespies Direct Method as in GillespieEnhanced
, the fast ones are handled by
tau leaping. This method can be a substancial improvement on speed when simulating a network
composed of different realms of magnitude (e.g. when simulating both gene regulation and
metabolism).
For references see J. Puchalka. and A.M. Kierzek, Briding the Gap betwwen Stochastic and Determininistic Regimes in the Kinetic Simulations of the Biochemical Reaction Networks, Biophysical 86, 1357-1372 (2004)
GillespieEnhanced
,
DependencyGraph
Nested Class Summary |
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Nested classes/interfaces inherited from class fern.simulation.Simulator |
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Simulator.FireType |
Constructor Summary | |
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HybridMaximalTimeStep(Network net)
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Method Summary | |
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String |
getName()
Gets the name of the algorithm. |
void |
initialize()
Initializes the algorithm: set t=0reset the AmountManager recalculate the propensities
Gets called at the very beginning of start |
void |
performStep(SimulationController control)
Performs one simulation step. |
void |
reinitialize()
Reset propensities when a event has been executed. |
void |
setAmount(int species,
long amount)
Sets the amount of the given species. |
void |
setVolume(double volume)
Sets the volume of the reaction network. |
Methods inherited from class fern.simulation.Simulator |
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addObserver, getAmount, getNet, getNextThetaEvent, getPropensity, getPropensityCalculator, getTime, getVolume, isInterpolateTheta, registerNewTheta, setInterpolateTheta, start, start |
Methods inherited from class java.lang.Object |
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equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public HybridMaximalTimeStep(Network net)
Method Detail |
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public void initialize()
Simulator
AmountManager
start
initialize
in class Simulator
public void reinitialize()
Simulator
reinitialize
in class Simulator
public void performStep(SimulationController control)
Simulator
Simulator.setAmount(int, long)
and Simulator.setVolume(double)
if they need correct values!
performStep
in class Simulator
control
- the simulators controllerpublic void setVolume(double volume)
Simulator
setVolume
in class Simulator
volume
- the volumepublic void setAmount(int species, long amount)
Simulator
setAmount
in class Simulator
species
- species indexamount
- amount of speciesAmountManager.setAmount(int, long)
public String getName()
Simulator
getName
in class Simulator
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