#include <AbstractWntOdeBasedCellCycleModel.hpp>

Inheritance diagram for AbstractWntOdeBasedCellCycleModel:

Collaboration diagram for AbstractWntOdeBasedCellCycleModel:

Public Member Functions
	AbstractWntOdeBasedCellCycleModel (boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())
	~AbstractWntOdeBasedCellCycleModel ()
void	ResetForDivision ()
void	UpdateCellProliferativeType ()
virtual void	ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel ()=0
double	GetAverageTransitCellCycleTime ()
double	GetAverageStemCellCycleTime ()
virtual bool	CanCellTerminallyDifferentiate ()
virtual void	OutputCellCycleModelParameters (out_stream &rParamsFile)
Protected Member Functions
double	GetWntLevel ()
void	UpdateCellCyclePhase ()
Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)
Friends
class	boost::serialization::access

Detailed Description

This class contains all the things common to the Wnt cell cycle ODE based models, the resetting method and updating of cell types etc.

The concrete models all need to operate with a WntConcentration singleton object.

These models have a constant length M phase, run ODEs to decide when to finish G1 phase, then add time for S and G2 phases (in some classes, random periods of time). The CellProliferativeType is updated dependent on the concentration of beta-catenin (given by one of the ODEs).

Definition at line 58 of file AbstractWntOdeBasedCellCycleModel.hpp.

Constructor & Destructor Documentation

AbstractWntOdeBasedCellCycleModel::AbstractWntOdeBasedCellCycleModel ( 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 38 of file AbstractWntOdeBasedCellCycleModel.cpp.

AbstractWntOdeBasedCellCycleModel::~AbstractWntOdeBasedCellCycleModel ( )

Destructor.

Definition at line 43 of file AbstractWntOdeBasedCellCycleModel.cpp.

Member Function Documentation

bool AbstractWntOdeBasedCellCycleModel::CanCellTerminallyDifferentiate ( ) [virtual]

Overridden CanCellTerminallyDifferentiate() method.

Reimplemented from AbstractCellCycleModel.

Definition at line 123 of file AbstractWntOdeBasedCellCycleModel.cpp.

virtual void AbstractWntOdeBasedCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel ( ) [pure virtual]

This must be implemented by subclasses to change cell type to reflect current levels of beta-catenin.

Implemented in AbstractVanLeeuwen2009WntSwatCellCycleModel, and WntCellCycleModel.

Referenced by UpdateCellProliferativeType().

double AbstractWntOdeBasedCellCycleModel::GetAverageStemCellCycleTime ( ) [virtual]

Overridden GetAverageStemCellCycleTime() method.

Reimplemented from AbstractCellCycleModel.

Definition at line 118 of file AbstractWntOdeBasedCellCycleModel.cpp.

double AbstractWntOdeBasedCellCycleModel::GetAverageTransitCellCycleTime ( ) [virtual]

Overridden GetAverageTransitCellCycleTime() method.

Reimplemented from AbstractCellCycleModel.

Definition at line 113 of file AbstractWntOdeBasedCellCycleModel.cpp.

double AbstractWntOdeBasedCellCycleModel::GetWntLevel ( ) [protected]

Get the Wnt level experienced by the cell.

Definition at line 47 of file AbstractWntOdeBasedCellCycleModel.cpp.

References WntConcentration< DIM >::GetWntLevel(), AbstractCellCycleModel::mDimension, AbstractCellCycleModel::mpCell, and NEVER_REACHED.

Referenced by WntCellCycleModel::AdjustOdeParameters(), AbstractVanLeeuwen2009WntSwatCellCycleModel::AdjustOdeParameters(), WntCellCycleModel::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), WntCellCycleModel::Initialise(), and AbstractVanLeeuwen2009WntSwatCellCycleModel::Initialise().

void AbstractWntOdeBasedCellCycleModel::OutputCellCycleModelParameters ( out_stream & rParamsFile ) [virtual]

Outputs cell-cycle model parameters to file.

Parameters:

rParamsFile the file stream to which the parameters are output

Reimplemented from AbstractOdeBasedCellCycleModel.

Reimplemented in AbstractVanLeeuwen2009WntSwatCellCycleModel, StochasticWntCellCycleModel, VanLeeuwen2009WntSwatCellCycleModelHypothesisOne, VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo, and WntCellCycleModel.

Definition at line 128 of file AbstractWntOdeBasedCellCycleModel.cpp.

void AbstractWntOdeBasedCellCycleModel::ResetForDivision ( ) [virtual]

Resets the Wnt Model to the start of the cell cycle (this model does not cycle naturally) Cells are given a new birth time and cell cycle proteins are reset. Note that the Wnt pathway proteins maintain their current values.

Should only be called by the Cell::Divide() method.

Reimplemented from AbstractOdeBasedCellCycleModel.

Reimplemented in StochasticWntCellCycleModel.

Definition at line 79 of file AbstractWntOdeBasedCellCycleModel.cpp.

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

template<class Archive >

void AbstractWntOdeBasedCellCycleModel::serialize	(	Archive &	archive,
		const unsigned int	version
	)		`[inline, private]`

Archive the cell-cycle model, never used directly - boost uses this.

Parameters:

archive	the archive
version	the current version of this class

Reimplemented from AbstractOdeBasedCellCycleModel.

Reimplemented in AbstractVanLeeuwen2009WntSwatCellCycleModel, StochasticWntCellCycleModel, VanLeeuwen2009WntSwatCellCycleModelHypothesisOne, VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo, and WntCellCycleModel.

Definition at line 71 of file AbstractWntOdeBasedCellCycleModel.hpp.

void AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase ( ) [protected, virtual]

Call base class UpdateCellCyclePhase, then UpdateCellProliferativeType.

Reimplemented from AbstractOdeBasedCellCycleModel.

Definition at line 95 of file AbstractWntOdeBasedCellCycleModel.cpp.

References AbstractOdeBasedCellCycleModel::GetOdeStopTime(), SimulationTime::Instance(), CellCycleModelOdeHandler::mLastTime, and UpdateCellProliferativeType().

void AbstractWntOdeBasedCellCycleModel::UpdateCellProliferativeType ( )

Updates the current cell type to reflect whether the beta-catenin level has dropped low enough to make it stop dividing. This should only be called when the cell-cycle model has been evaluated to the current time, or it may give misleading results.

Definition at line 106 of file AbstractWntOdeBasedCellCycleModel.cpp.

References ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel(), AbstractCellCycleModel::mpCell, and CellCycleModelOdeHandler::mpOdeSystem.

Referenced by UpdateCellCyclePhase().

Friends And Related Function Documentation

friend class boost::serialization::access [friend]

Needed for serialization.

Reimplemented from AbstractOdeBasedCellCycleModel.

Reimplemented in AbstractVanLeeuwen2009WntSwatCellCycleModel, StochasticWntCellCycleModel, VanLeeuwen2009WntSwatCellCycleModelHypothesisOne, VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo, and WntCellCycleModel.

Definition at line 63 of file AbstractWntOdeBasedCellCycleModel.hpp.

The documentation for this class was generated from the following files:

crypt/src/cell/cycle/AbstractWntOdeBasedCellCycleModel.hpp
crypt/src/cell/cycle/AbstractWntOdeBasedCellCycleModel.cpp

Public Member Functions

Protected Member Functions

Private Member Functions

Friends

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation