AbstractVanLeeuwen2009WntSwatCellCycleModel Class Reference

#include <AbstractVanLeeuwen2009WntSwatCellCycleModel.hpp>

Inherits AbstractWntOdeBasedCellCycleModel.

Inherited by VanLeeuwen2009WntSwatCellCycleModelHypothesisOne, and VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo.

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)
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

Detailed Description

Wnt-dependent cell-cycle model.

Definition at line 46 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 32 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.cpp.

Member Function Documentation

void AbstractVanLeeuwen2009WntSwatCellCycleModel::AdjustOdeParameters ( double currentTime ) [private, virtual]

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 71 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.cpp.

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

void AbstractVanLeeuwen2009WntSwatCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel ( ) [private, virtual]

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 37 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.cpp.

References AbstractCellCycleModel::mCellProliferativeType, 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 85 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.cpp.

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

Referenced by CryptSimulation2d::WriteBetaCatenin().

double AbstractVanLeeuwen2009WntSwatCellCycleModel::GetMembraneBoundBetaCateninLevel ( )

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

Definition at line 80 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.cpp.

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

Referenced by LinearSpringWithVariableSpringConstantsForce< DIM >::VariableSpringConstantMultiplicationFactor(), and CryptSimulation2d::WriteBetaCatenin().

double AbstractVanLeeuwen2009WntSwatCellCycleModel::GetNuclearBetaCateninLevel ( )

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

Definition at line 92 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.cpp.

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

Referenced by CryptSimulation2d::WriteBetaCatenin().

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 57 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: