#include <AbstractVanLeeuwen2009WntSwatCellCycleModel.hpp>

Inheritance diagram for AbstractVanLeeuwen2009WntSwatCellCycleModel:

Collaboration diagram for AbstractVanLeeuwen2009WntSwatCellCycleModel:

Public Member Functions
	AbstractVanLeeuwen2009WntSwatCellCycleModel (boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())

void	Initialise ()

double	GetMembraneBoundBetaCateninLevel ()

double	GetCytoplasmicBetaCateninLevel ()

double	GetNuclearBetaCateninLevel ()

virtual void	InitialiseOdeSystem (double wntConcentration, boost::shared_ptr< AbstractCellMutationState > pMutationState)=0

virtual void	OutputCellCycleModelParameters (out_stream &rParamsFile)

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

virtual	~AbstractWntOdeBasedCellCycleModel ()

void	ResetForDivision ()

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	GetG2Duration () 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)

virtual void	InitialiseDaughterCell ()

CellPtr	GetCell ()

void	SetDimension (unsigned dimension)

unsigned	GetDimension () const

double	GetBirthTime () const

double	GetAge ()

virtual AbstractCellCycleModel *	CreateCellCycleModel ()=0

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
	AbstractVanLeeuwen2009WntSwatCellCycleModel (const AbstractVanLeeuwen2009WntSwatCellCycleModel &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	ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel ()

void	AdjustOdeParameters (double currentTime)

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.

Definition at line 53 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.hpp.

Constructor & Destructor Documentation

AbstractVanLeeuwen2009WntSwatCellCycleModel::AbstractVanLeeuwen2009WntSwatCellCycleModel ( const AbstractVanLeeuwen2009WntSwatCellCycleModel & 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 46 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.cpp.

AbstractVanLeeuwen2009WntSwatCellCycleModel::AbstractVanLeeuwen2009WntSwatCellCycleModel ( boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver = boost::shared_ptr<AbstractCellCycleModelOdeSolver>() )

Default constructor.

Parameters

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

Definition at line 41 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.cpp.

Member Function Documentation

void AbstractVanLeeuwen2009WntSwatCellCycleModel::AdjustOdeParameters ( double currentTime )

privatevirtual

Adjust any ODE parameters needed before solving until currentTime.

Parameters

currentTime the time up to which the system will be solved.

Reimplemented from CellCycleModelOdeHandler.

Definition at line 111 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.cpp.

References AbstractWntOdeBasedCellCycleModel::GetWntLevel(), AbstractCellCycleModel::mpCell, CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().

void AbstractVanLeeuwen2009WntSwatCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel ( )

privatevirtual

Called by Initialise() and UpdateCellProliferativeType() only. Updates mCellProliferativeType to match mpOdeSystem's beta-catenin levels

This carries out the work for UpdateCellProliferativeType(); But does not check the current time so it can be used by the initialise method.

Implements AbstractWntOdeBasedCellCycleModel.

Definition at line 64 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.cpp.

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

Referenced by Initialise().

double AbstractVanLeeuwen2009WntSwatCellCycleModel::GetCytoplasmicBetaCateninLevel ( )

Returns: the level of cytoplasmic beta-catenin (including ubiquitinated - awaiting degradation)

Definition at line 125 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.cpp.

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

Referenced by CellBetaCateninWriter< ELEMENT_DIM, SPACE_DIM >::GetCellDataForVtkOutput(), and CellBetaCateninWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell().

double AbstractVanLeeuwen2009WntSwatCellCycleModel::GetMembraneBoundBetaCateninLevel ( )

Returns: the level of membrane bound beta-catenin. To be used in cell-cell adhesion calculations.

Definition at line 120 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.cpp.

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

Referenced by LinearSpringWithVariableSpringConstantsForce< DIM >::VariableSpringConstantMultiplicationFactor(), and CellBetaCateninWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell().

double AbstractVanLeeuwen2009WntSwatCellCycleModel::GetNuclearBetaCateninLevel ( )

Returns: the level of nuclear beta-catenin. To be used in transcription

Definition at line 132 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.cpp.

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

Referenced by CellBetaCateninWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell().

void AbstractVanLeeuwen2009WntSwatCellCycleModel::Initialise ( void )

virtual

See AbstractCellCycleModel::Initialise()

In this case we set up a new ODE system for a daughter cell.

Reimplemented from AbstractCellCycleModel.

Definition at line 97 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.cpp.

References ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel(), AbstractParameterisedSystem< VECTOR >::GetInitialConditions(), AbstractWntOdeBasedCellCycleModel::GetWntLevel(), InitialiseOdeSystem(), AbstractCellCycleModel::mpCell, CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::SetStateVariables().

virtual void AbstractVanLeeuwen2009WntSwatCellCycleModel::InitialiseOdeSystem	(	double	wntConcentration,
		boost::shared_ptr< AbstractCellMutationState >	pMutationState
	)