#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 AbstractOdeBasedCellCycleModel
	AbstractOdeBasedCellCycleModel (double lastTime=SimulationTime::Instance() ->GetTime(), boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())

virtual	~AbstractOdeBasedCellCycleModel ()

double	GetOdeStopTime ()

void	SetBirthTime (double birthTime)

std::vector< double >	GetProteinConcentrations () const

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

void	SetFinishedRunningOdes (bool finishedRunningOdes)

void	SetDivideTime (double divideTime)

void	SetG2PhaseStartTime (double g2PhaseStartTime)

Public Member Functions inherited from AbstractCellCycleModel
	AbstractCellCycleModel ()

virtual	~AbstractCellCycleModel ()

void	SetCell (CellPtr pCell)

virtual void	InitialiseDaughterCell ()

CellPtr	GetCell ()

void	SetDimension (unsigned dimension)

unsigned	GetDimension ()

double	GetBirthTime () const

double	GetAge ()

virtual bool	ReadyToDivide ()

virtual AbstractCellCycleModel *	CreateCellCycleModel ()=0

CellCyclePhase	GetCurrentCellCyclePhase ()

virtual double	GetG1Duration ()

double	GetStemCellG1Duration ()

double	GetTransitCellG1Duration ()

double	GetSG2MDuration ()

virtual double	GetSDuration ()

virtual double	GetG2Duration ()

virtual double	GetMDuration ()

virtual void	SetStemCellG1Duration (double stemCellG1Duration)

virtual void	SetTransitCellG1Duration (double transitCellG1Duration)

void	SetSDuration (double sDuration)

void	SetG2Duration (double g2Duration)

void	SetMDuration (double mDuration)

double	GetMinimumGapDuration ()

void	SetMinimumGapDuration (double minimumGapDuration)

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)

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 Member Functions inherited from AbstractWntOdeBasedCellCycleModel
double	GetWntLevel ()

void	UpdateCellCyclePhase ()

Protected Member Functions inherited from CellCycleModelOdeHandler
bool	SolveOdeToTime (double currentTime)

Protected Attributes inherited from AbstractOdeBasedCellCycleModel
double	mDivideTime

bool	mFinishedRunningOdes

double	mG2PhaseStartTime

Protected Attributes inherited from AbstractCellCycleModel
CellPtr	mpCell

double	mBirthTime

CellCyclePhase	mCurrentCellCyclePhase

double	mG1Duration

bool	mReadyToDivide

unsigned	mDimension

double	mMinimumGapDuration

double	mStemCellG1Duration

double	mTransitCellG1Duration

double	mSDuration

double	mG2Duration

double	mMDuration

Protected Attributes inherited from CellCycleModelOdeHandler
double	mDt

AbstractOdeSystem *	mpOdeSystem

boost::shared_ptr < AbstractCellCycleModelOdeSolver >	mpOdeSolver

double	mLastTime

Detailed Description

Wnt-dependent cell-cycle model.

Definition at line 53 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.hpp.

Constructor & Destructor Documentation

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 39 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 91 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 44 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 105 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 100 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 112 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 77 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
	)

pure virtual

Pure virtual method to be implemented in concrete classes, which should should allocate the mOdeSystem variable using the appropriate hypothesis (one or two).

Parameters