#include <SingleOdeWntCellCycleModel.hpp>

Inheritance diagram for SingleOdeWntCellCycleModel:

Collaboration diagram for SingleOdeWntCellCycleModel:

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

void	Initialise ()

void	UpdateCellCyclePhase ()

AbstractCellCycleModel *	CreateCellCycleModel ()

double	GetBetaCateninConcentration ()

void	SetBetaCateninDivisionThreshold (double betaCateninDivisionThreshold)

double	GetBetaCateninDivisionThreshold ()

virtual void	OutputCellCycleModelParameters (out_stream &rParamsFile)

Public Member Functions inherited from SimpleWntCellCycleModel
	SimpleWntCellCycleModel ()

virtual void	InitialiseDaughterCell ()

bool	GetUseCellProliferativeTypeDependentG1Duration () const

void	SetUseCellProliferativeTypeDependentG1Duration (bool useCellProliferativeTypeDependentG1Duration=true)

virtual bool	CanCellTerminallyDifferentiate ()

double	GetWntStemThreshold () const

void	SetWntStemThreshold (double wntStemThreshold)

double	GetWntTransitThreshold () const

void	SetWntTransitThreshold (double wntTransitThreshold)

double	GetWntLabelledThreshold () const

void	SetWntLabelledThreshold (double wntLabelledThreshold)

Public Member Functions inherited from AbstractSimplePhaseBasedCellCycleModel
	AbstractSimplePhaseBasedCellCycleModel ()

virtual	~AbstractSimplePhaseBasedCellCycleModel ()

virtual void	ResetForDivision ()

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)

virtual double	GetAverageTransitCellCycleTime ()

virtual double	GetAverageStemCellCycleTime ()

double	GetMinimumGapDuration () const

void	SetMinimumGapDuration (double minimumGapDuration)

Public Member Functions inherited from AbstractCellCycleModel
	AbstractCellCycleModel ()

virtual	~AbstractCellCycleModel ()

void	SetCell (CellPtr pCell)

CellPtr	GetCell ()

virtual void	SetBirthTime (double birthTime)

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
	SingleOdeWntCellCycleModel (const SingleOdeWntCellCycleModel &rModel)

Protected Member Functions inherited from SimpleWntCellCycleModel
double	GetWntLevel () const

WntConcentrationType	GetWntType ()

void	SetG1Duration ()

	SimpleWntCellCycleModel (const SimpleWntCellCycleModel &rModel)

Protected Member Functions inherited from AbstractSimplePhaseBasedCellCycleModel
	AbstractSimplePhaseBasedCellCycleModel (const AbstractSimplePhaseBasedCellCycleModel &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 ()

virtual void	AdjustOdeParameters (double currentTime)

Private Attributes
double	mBetaCateninDivisionThreshold

Friends
class	boost::serialization::access

Additional Inherited Members
Protected Attributes inherited from SimpleWntCellCycleModel
bool	mUseCellProliferativeTypeDependentG1Duration

double	mWntStemThreshold

double	mWntTransitThreshold

double	mWntLabelledThreshold

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. Needs to operate with a WntConcentration singleton object.

This model has a constant length M phase, runs ODEs to decide when to finish G1 phase then adds time for S and G2 phases. The CellProliferativeType is updated dependent on the concentration of beta-catenin (given by one of the ODEs).

Definition at line 58 of file SingleOdeWntCellCycleModel.hpp.

Constructor & Destructor Documentation

SingleOdeWntCellCycleModel::SingleOdeWntCellCycleModel ( const SingleOdeWntCellCycleModel & 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 60 of file SingleOdeWntCellCycleModel.cpp.

References CellCycleModelOdeHandler::GetOdeSystem(), SimpleWntCellCycleModel::GetWntLevel(), AbstractCellCycleModel::mpCell, AbstractParameterisedSystem< VECTOR >::rGetStateVariables(), CellCycleModelOdeHandler::SetOdeSystem(), and CellCycleModelOdeHandler::SetStateVariables().

Referenced by CreateCellCycleModel().

SingleOdeWntCellCycleModel::SingleOdeWntCellCycleModel ( 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 SingleOdeWntCellCycleModel.cpp.

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

Member Function Documentation

void SingleOdeWntCellCycleModel::AdjustOdeParameters ( double currentTime )

privatevirtual

Adjust any ODE parameters needed before solving until currentTime. Defaults to do nothing.

Parameters

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

Reimplemented from CellCycleModelOdeHandler.

Definition at line 122 of file SingleOdeWntCellCycleModel.cpp.

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

void SingleOdeWntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel ( )

private

Called by Initialise() and UpdateCellProliferativeType() only. Updates the mpCell::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.

Definition at line 131 of file SingleOdeWntCellCycleModel.cpp.

References GetBetaCateninConcentration(), GetBetaCateninDivisionThreshold(), AbstractCellCycleModel::mpCell, and CellCycleModelOdeHandler::mpOdeSystem.

Referenced by Initialise(), and UpdateCellCyclePhase().

AbstractCellCycleModel * SingleOdeWntCellCycleModel::CreateCellCycleModel ( )

virtual

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

Returns: the new cell-cycle model

Reimplemented from SimpleWntCellCycleModel.

Definition at line 89 of file SingleOdeWntCellCycleModel.cpp.

References SingleOdeWntCellCycleModel().

double SingleOdeWntCellCycleModel::GetBetaCateninConcentration ( )

Returns: the total beta-catenin concentration

Definition at line 159 of file SingleOdeWntCellCycleModel.cpp.

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

Referenced by ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel().

double SingleOdeWntCellCycleModel::GetBetaCateninDivisionThreshold ( )

Returns: mBetaCateninDivisionThreshold.

Definition at line 169 of file SingleOdeWntCellCycleModel.cpp.

References mBetaCateninDivisionThreshold.

Referenced by ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel().

void SingleOdeWntCellCycleModel::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 AbstractSimplePhaseBasedCellCycleModel.

Definition at line 102 of file SingleOdeWntCellCycleModel.cpp.

References ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel(), AbstractParameterisedSystem< VECTOR >::GetInitialConditions(), SimpleWntCellCycleModel::GetWntLevel(), AbstractSimplePhaseBasedCellCycleModel::Initialise(), AbstractCellCycleModel::mBirthTime, AbstractCellCycleModel::mpCell, CellCycleModelOdeHandler::mpOdeSystem, CellCycleModelOdeHandler::SetLastTime(), and AbstractParameterisedSystem< VECTOR >::SetStateVariables().