DeltaNotchCellCycleModel Class Reference

#include <DeltaNotchCellCycleModel.hpp>

Inherits StochasticDurationGenerationBasedCellCycleModel, and CellCycleModelOdeHandler.

Collaboration diagram for DeltaNotchCellCycleModel:
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List of all members.

Public Member Functions

 DeltaNotchCellCycleModel (boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())
AbstractCellCycleModel * CreateCellCycleModel ()
void Initialise ()
void SetInitialConditions (std::vector< double > initialConditions)
void UpdateCellCyclePhase ()
void UpdateDeltaNotch ()
double GetNotch ()
double GetDelta ()
double GetMeanNeighbouringDelta ()
virtual void OutputCellCycleModelParameters (out_stream &rParamsFile)

Private Member Functions

template<class Archive >
void serialize (Archive &archive, const unsigned int version)

Private Attributes

std::vector< double > mInitialConditions

Friends

class boost::serialization::access

Detailed Description

A subclass of StochasticDurationGenerationBasedCellCycleModel that includes a Delta-Notch ODE system.

For another example of a cell cycle model that is not *based on* an ODE system, but that includes an ODE system, see SingleOdeWntCellCycleModel (in Crypt).

Definition at line 55 of file DeltaNotchCellCycleModel.hpp.

Constructor & Destructor Documentation

DeltaNotchCellCycleModel::DeltaNotchCellCycleModel ( boost::shared_ptr< AbstractCellCycleModelOdeSolver >  pOdeSolver = boost::shared_ptr<AbstractCellCycleModelOdeSolver>()  ) 

Default constructor calls base class.

Parameters:
pOdeSolver An optional pointer to a cell-cycle model ODE solver object (allows the use of different ODE solvers)

Definition at line 44 of file DeltaNotchCellCycleModel.cpp.

References CellCycleModelOdeHandler::mpOdeSolver, and CellCycleModelOdeHandler::SetDt().

Referenced by CreateCellCycleModel().

Member Function Documentation

AbstractCellCycleModel * DeltaNotchCellCycleModel::CreateCellCycleModel (  )  [virtual]

Overridden builder method to create new copies of this cell-cycle model.

Returns:
Returns a copy of the current cell cycle model.

Reimplemented from StochasticDurationGenerationBasedCellCycleModel.

Definition at line 62 of file DeltaNotchCellCycleModel.cpp.

References DeltaNotchCellCycleModel(), GetMeanNeighbouringDelta(), CellCycleModelOdeHandler::GetOdeSystem(), AbstractCellCycleModel::mBirthTime, AbstractCellCycleModel::mDimension, AbstractSimpleGenerationBasedCellCycleModel::mGeneration, CellCycleModelOdeHandler::mLastTime, AbstractSimpleGenerationBasedCellCycleModel::mMaxTransitGenerations, CellCycleModelOdeHandler::mpOdeSolver, CellCycleModelOdeHandler::mpOdeSystem, AbstractParameterisedSystem< VECTOR >::rGetStateVariables(), AbstractCellCycleModel::SetBirthTime(), AbstractCellCycleModel::SetDimension(), AbstractSimpleGenerationBasedCellCycleModel::SetGeneration(), CellCycleModelOdeHandler::SetLastTime(), AbstractSimpleGenerationBasedCellCycleModel::SetMaxTransitGenerations(), CellCycleModelOdeHandler::SetOdeSystem(), AbstractParameterisedSystem< VECTOR >::SetParameter(), and CellCycleModelOdeHandler::SetStateVariables().

double DeltaNotchCellCycleModel::GetDelta (  ) 
Returns:
Returns the current Delta level in this cell.

Definition at line 137 of file DeltaNotchCellCycleModel.cpp.

References CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().

Referenced by DeltaNotchTrackingModifier< DIM >::UpdateCellData().

double DeltaNotchCellCycleModel::GetMeanNeighbouringDelta (  ) 
Returns:
Get the current level of Delta neighbouring the cell.

Definition at line 144 of file DeltaNotchCellCycleModel.cpp.

References AbstractParameterisedSystem< VECTOR >::GetParameter(), and CellCycleModelOdeHandler::mpOdeSystem.

Referenced by CreateCellCycleModel().

double DeltaNotchCellCycleModel::GetNotch (  ) 
Returns:
Returns the current Notch level in this cell.

Definition at line 130 of file DeltaNotchCellCycleModel.cpp.

References CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().

Referenced by DeltaNotchTrackingModifier< DIM >::UpdateCellData().

void DeltaNotchCellCycleModel::Initialise ( void   )  [virtual]

Initialise the cell-cycle model at the start of a simulation.

This overridden method sets up a new Delta-Notch ODE system.

Reimplemented from AbstractSimpleCellCycleModel.

Definition at line 94 of file DeltaNotchCellCycleModel.cpp.

References AbstractParameterisedSystem< VECTOR >::GetInitialConditions(), AbstractCellCycleModel::mBirthTime, mInitialConditions, AbstractCellCycleModel::mpCell, CellCycleModelOdeHandler::mpOdeSystem, CellCycleModelOdeHandler::SetLastTime(), and AbstractParameterisedSystem< VECTOR >::SetStateVariables().

void DeltaNotchCellCycleModel::OutputCellCycleModelParameters ( out_stream &  rParamsFile  )  [virtual]

Outputs cell-cycle model parameters to file.

Parameters:
rParamsFile the file stream to which the parameters are output

Reimplemented from StochasticDurationGenerationBasedCellCycleModel.

Definition at line 151 of file DeltaNotchCellCycleModel.cpp.

template<class Archive >
void DeltaNotchCellCycleModel::serialize ( Archive &  archive,
const unsigned int  version 
) [inline, private]

Archive the cell-cycle model and member variables.

Parameters:
archive the archive
version the current version of this class

Reimplemented from CellCycleModelOdeHandler.

Definition at line 68 of file DeltaNotchCellCycleModel.hpp.

void DeltaNotchCellCycleModel::SetInitialConditions ( std::vector< double >  initialConditions  ) 

Set the initial conditions for delta, notch, mean_delta.

Parameters:
initialConditions are the initial conditions

Definition at line 115 of file DeltaNotchCellCycleModel.cpp.

References mInitialConditions.

void DeltaNotchCellCycleModel::UpdateCellCyclePhase (  )  [virtual]

Overridden UpdateCellCyclePhase() method.

Reimplemented from AbstractSimpleCellCycleModel.

Definition at line 86 of file DeltaNotchCellCycleModel.cpp.

References SimulationTime::Instance(), CellCycleModelOdeHandler::SolveOdeToTime(), and UpdateDeltaNotch().

void DeltaNotchCellCycleModel::UpdateDeltaNotch (  ) 

Update the current levels of Delta and Notch in the cell.

Definition at line 121 of file DeltaNotchCellCycleModel.cpp.

References AbstractCellCycleModel::mpCell, CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::SetParameter().

Referenced by UpdateCellCyclePhase().

Friends And Related Function Documentation

friend class boost::serialization::access [friend]

Needed for serialization.

Reimplemented from CellCycleModelOdeHandler.

Definition at line 60 of file DeltaNotchCellCycleModel.hpp.

Member Data Documentation

std::vector<double> DeltaNotchCellCycleModel::mInitialConditions [private]

The initial condition for delta, notch, mean_delta

Definition at line 77 of file DeltaNotchCellCycleModel.hpp.

Referenced by Initialise(), and SetInitialConditions().

The documentation for this class was generated from the following files:
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