AbstractWntOdeBasedCellCycleModel Class Reference

#include <AbstractWntOdeBasedCellCycleModel.hpp>

Inheritance diagram for AbstractWntOdeBasedCellCycleModel:

Collaboration diagram for AbstractWntOdeBasedCellCycleModel:

List of all members.

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 50 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 31 of file AbstractWntOdeBasedCellCycleModel.cpp.

AbstractWntOdeBasedCellCycleModel::~AbstractWntOdeBasedCellCycleModel ( )

Destructor.

Definition at line 36 of file AbstractWntOdeBasedCellCycleModel.cpp.

Member Function Documentation

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 63 of file AbstractWntOdeBasedCellCycleModel.hpp.

double AbstractWntOdeBasedCellCycleModel::GetWntLevel ( ) [protected]

Get the Wnt level experienced by the cell.

Definition at line 40 of file AbstractWntOdeBasedCellCycleModel.cpp.

References WntConcentration< DIM >::GetWntLevel(), WntConcentration< DIM >::Instance(), 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::UpdateCellCyclePhase ( ) [protected, virtual]

Call base class UpdateCellCyclePhase, then UpdateCellProliferativeType.

Reimplemented from AbstractOdeBasedCellCycleModel.

Definition at line 88 of file AbstractWntOdeBasedCellCycleModel.cpp.

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

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 72 of file AbstractWntOdeBasedCellCycleModel.cpp.

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

Referenced by StochasticWntCellCycleModel::ResetForDivision().

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 99 of file AbstractWntOdeBasedCellCycleModel.cpp.

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

Referenced by UpdateCellCyclePhase().

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::GetAverageTransitCellCycleTime ( ) [virtual]

Overridden GetAverageTransitCellCycleTime() method.

Reimplemented from AbstractCellCycleModel.

Definition at line 106 of file AbstractWntOdeBasedCellCycleModel.cpp.

double AbstractWntOdeBasedCellCycleModel::GetAverageStemCellCycleTime ( ) [virtual]

Overridden GetAverageStemCellCycleTime() method.

Reimplemented from AbstractCellCycleModel.

Definition at line 111 of file AbstractWntOdeBasedCellCycleModel.cpp.

bool AbstractWntOdeBasedCellCycleModel::CanCellTerminallyDifferentiate ( ) [virtual]

Overridden CanCellTerminallyDifferentiate() method.

Reimplemented from AbstractCellCycleModel.

Definition at line 116 of file AbstractWntOdeBasedCellCycleModel.cpp.

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 121 of file AbstractWntOdeBasedCellCycleModel.cpp.

References AbstractOdeBasedCellCycleModel::OutputCellCycleModelParameters().

Referenced by WntCellCycleModel::OutputCellCycleModelParameters(), and AbstractVanLeeuwen2009WntSwatCellCycleModel::OutputCellCycleModelParameters().

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 55 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
	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