#include <StochasticWntCellCycleModel.hpp>

Inheritance diagram for StochasticWntCellCycleModel:

Collaboration diagram for StochasticWntCellCycleModel:

Public Member Functions
	StochasticWntCellCycleModel (boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())

virtual	~StochasticWntCellCycleModel ()

AbstractCellCycleModel *	CreateCellCycleModel ()

void	InitialiseDaughterCell ()

void	Initialise ()

void	ResetForDivision ()

double	GetG2Duration () const

virtual void	OutputCellCycleModelParameters (out_stream &rParamsFile)

Public Member Functions inherited from WntCellCycleModel
	WntCellCycleModel (boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())

	~WntCellCycleModel ()

AbstractCellCycleModel *	CreateCellCycleModel ()

void	Initialise ()

Public Member Functions inherited from AbstractWntOdeBasedCellCycleModel
	AbstractWntOdeBasedCellCycleModel (boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())

virtual	~AbstractWntOdeBasedCellCycleModel ()

void	UpdateCellProliferativeType ()

double	GetAverageTransitCellCycleTime ()

double	GetAverageStemCellCycleTime ()

virtual bool	CanCellTerminallyDifferentiate ()

Public Member Functions inherited from AbstractOdeBasedPhaseBasedCellCycleModel
	AbstractOdeBasedPhaseBasedCellCycleModel (double lastTime=SimulationTime::Instance() ->GetTime(), boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())

virtual	~AbstractOdeBasedPhaseBasedCellCycleModel ()

double	GetOdeStopTime ()

void	SetBirthTime (double birthTime)

Public Member Functions inherited from AbstractPhaseBasedCellCycleModel
	AbstractPhaseBasedCellCycleModel ()

virtual	~AbstractPhaseBasedCellCycleModel ()

virtual bool	ReadyToDivide ()

CellCyclePhase	GetCurrentCellCyclePhase () const

virtual double	GetG1Duration () const

double	GetStemCellG1Duration () const

double	GetTransitCellG1Duration () const

double	GetSG2MDuration () const

virtual double	GetSDuration () const

virtual double	GetMDuration () const

virtual void	SetStemCellG1Duration (double stemCellG1Duration)

virtual void	SetTransitCellG1Duration (double transitCellG1Duration)

void	SetSDuration (double sDuration)

void	SetG2Duration (double g2Duration)

void	SetMDuration (double mDuration)

double	GetMinimumGapDuration () const

void	SetMinimumGapDuration (double minimumGapDuration)

Public Member Functions inherited from AbstractCellCycleModel
	AbstractCellCycleModel ()

virtual	~AbstractCellCycleModel ()

void	SetCell (CellPtr pCell)

CellPtr	GetCell ()

void	SetDimension (unsigned dimension)

unsigned	GetDimension () const

double	GetBirthTime () const

double	GetAge ()

void	OutputCellCycleModelInfo (out_stream &rParamsFile)

Public Member Functions inherited from Identifiable
virtual	~Identifiable ()

std::string	GetIdentifier () const

Public Member Functions inherited from CellCycleModelOdeHandler
	CellCycleModelOdeHandler (double lastTime=SimulationTime::Instance() ->GetTime(), boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())

virtual	~CellCycleModelOdeHandler ()

AbstractOdeSystem *	GetOdeSystem () const

void	SetOdeSystem (AbstractOdeSystem *pOdeSystem)

const boost::shared_ptr< AbstractCellCycleModelOdeSolver >	GetOdeSolver () const

void	SetLastTime (double lastTime)

double	GetDt ()

void	SetDt (double timeStep)

void	SetStateVariables (const std::vector< double > &rStateVariables)

std::vector< double >	GetProteinConcentrations () const

void	SetProteinConcentrationsForTestsOnly (double lastTime, std::vector< double > proteinConcentrations)

Protected Member Functions
	StochasticWntCellCycleModel (const StochasticWntCellCycleModel &rModel)

Protected Member Functions inherited from WntCellCycleModel
	WntCellCycleModel (const WntCellCycleModel &rModel)

Protected Member Functions inherited from AbstractWntOdeBasedCellCycleModel
double	GetWntLevel () const

void	UpdateCellCyclePhase ()

	AbstractWntOdeBasedCellCycleModel (const AbstractWntOdeBasedCellCycleModel &rModel)

Protected Member Functions inherited from AbstractOdeBasedPhaseBasedCellCycleModel
	AbstractOdeBasedPhaseBasedCellCycleModel (const AbstractOdeBasedPhaseBasedCellCycleModel &rModel)

Protected Member Functions inherited from AbstractPhaseBasedCellCycleModel
	AbstractPhaseBasedCellCycleModel (const AbstractPhaseBasedCellCycleModel &rModel)

Protected Member Functions inherited from AbstractCellCycleModel
	AbstractCellCycleModel (const AbstractCellCycleModel &rModel)

Protected Member Functions inherited from CellCycleModelOdeHandler
	CellCycleModelOdeHandler (const CellCycleModelOdeHandler &rHandler)

bool	SolveOdeToTime (double currentTime)

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

void	GenerateStochasticG2Duration ()

Private Attributes
double	mStochasticG2Duration

Friends
class	boost::serialization::access

Additional Inherited Members
Protected Attributes inherited from AbstractOdeBasedPhaseBasedCellCycleModel
double	mDivideTime

double	mG2PhaseStartTime

Protected Attributes inherited from AbstractPhaseBasedCellCycleModel
CellCyclePhase	mCurrentCellCyclePhase

double	mG1Duration

double	mMinimumGapDuration

double	mStemCellG1Duration

double	mTransitCellG1Duration

double	mSDuration

double	mG2Duration

double	mMDuration

Protected Attributes inherited from AbstractCellCycleModel
CellPtr	mpCell

double	mBirthTime

bool	mReadyToDivide

unsigned	mDimension

Protected Attributes inherited from CellCycleModelOdeHandler
double	mDt

AbstractOdeSystem *	mpOdeSystem

boost::shared_ptr< AbstractCellCycleModelOdeSolver >	mpOdeSolver

double	mLastTime

bool	mFinishedRunningOdes

Detailed Description

Wnt-dependent cell-cycle model with a stochastic G2 duration.

Note that this class uses C++'s default copying semantics, and so doesn't implement a copy constructor or operator=.

Definition at line 51 of file StochasticWntCellCycleModel.hpp.

Constructor & Destructor Documentation

StochasticWntCellCycleModel::StochasticWntCellCycleModel ( const StochasticWntCellCycleModel & rModel )

protected

Protected copy-constructor for use by CreateCellCycleModel. The only way for external code to create a copy of a cell cycle model is by calling that method, to ensure that a model of the correct subclass is created. This copy-constructor helps subclasses to ensure that all member variables are correctly copied when this happens.

This method is called by child classes to set member variables for a daughter cell upon cell division. Note that the parent cell cycle model will have had ResetForDivision() called just before CreateCellCycleModel() is called, so performing an exact copy of the parent is suitable behaviour. Any daughter-cell-specific initialisation can be done in InitialiseDaughterCell().

Parameters

rModel the cell cycle model to copy.

Definition at line 59 of file StochasticWntCellCycleModel.cpp.

Referenced by CreateCellCycleModel().

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

The standard constructor called in tests.

Parameters

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

Definition at line 38 of file StochasticWntCellCycleModel.cpp.

References CellCycleModelOdeSolver< CELL_CYCLE_MODEL, ODE_SOLVER >::Instance(), and CellCycleModelOdeHandler::mpOdeSolver.

StochasticWntCellCycleModel::~StochasticWntCellCycleModel ( )

virtual

Empty virtual destructor so archiving works with static libraries.

Definition at line 56 of file StochasticWntCellCycleModel.cpp.

Member Function Documentation

AbstractCellCycleModel * StochasticWntCellCycleModel::CreateCellCycleModel ( )

virtual

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

Returns: the new cell-cycle model

Implements AbstractCellCycleModel.

Definition at line 124 of file StochasticWntCellCycleModel.cpp.

References StochasticWntCellCycleModel().

void StochasticWntCellCycleModel::GenerateStochasticG2Duration ( )

private

This method introduces the stochastic element of this class.

We allow the duration of the G2 phase of the cell cycle to vary as a normal random deviate with a mean of its deterministic duration, a standard deviation of 0.9 hours, and a cutoff to ensure that it is greater than some minimum value.

Definition at line 86 of file StochasticWntCellCycleModel.cpp.

References AbstractPhaseBasedCellCycleModel::GetG2Duration(), RandomNumberGenerator::Instance(), AbstractPhaseBasedCellCycleModel::mMinimumGapDuration, mStochasticG2Duration, and RandomNumberGenerator::NormalRandomDeviate().

Referenced by Initialise(), InitialiseDaughterCell(), and ResetForDivision().

double StochasticWntCellCycleModel::GetG2Duration ( ) const

virtual

Returns: the duration of the G2 phase.

Reimplemented from AbstractPhaseBasedCellCycleModel.

Definition at line 119 of file StochasticWntCellCycleModel.cpp.

References mStochasticG2Duration.

void StochasticWntCellCycleModel::Initialise ( void )

virtual

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

This overridden method sets up a new WntCellCycleOdeSystem, sets the cell type according to the current beta catenin level and sets a random G2 duration.

Reimplemented from AbstractCellCycleModel.

Definition at line 107 of file StochasticWntCellCycleModel.cpp.

References GenerateStochasticG2Duration(), and WntCellCycleModel::Initialise().

void StochasticWntCellCycleModel::InitialiseDaughterCell ( )

virtual

Set the duration of the G2 phase for the daughter cell.

Reimplemented from AbstractCellCycleModel.

Definition at line 101 of file StochasticWntCellCycleModel.cpp.

References GenerateStochasticG2Duration(), and AbstractCellCycleModel::InitialiseDaughterCell().

void StochasticWntCellCycleModel::OutputCellCycleModelParameters ( out_stream & rParamsFile )

virtual

Overridden OutputCellCycleModelParameters() method.