SimpleOxygenBasedCellCycleModel Class Reference

#include <SimpleOxygenBasedCellCycleModel.hpp>

Inherited by StochasticOxygenBasedCellCycleModel.

Collaboration diagram for SimpleOxygenBasedCellCycleModel:

Public Member Functions
	SimpleOxygenBasedCellCycleModel ()
void	UpdateCellCyclePhase ()
void	UpdateHypoxicDuration ()
double	GetCurrentHypoxicDuration ()
double	GetCurrentHypoxiaOnsetTime ()
AbstractCellCycleModel *	CreateCellCycleModel ()
double	GetHypoxicConcentration ()
void	SetHypoxicConcentration (double hypoxicConcentration)
double	GetQuiescentConcentration ()
void	SetQuiescentConcentration (double quiescentConcentration)
double	GetCriticalHypoxicDuration ()
void	SetCriticalHypoxicDuration (double criticalHypoxicDuration)
void	SetCurrentHypoxiaOnsetTime (double currentHypoxiaOnsetTime)
virtual void	OutputCellCycleModelParameters (out_stream &rParamsFile)
Protected Attributes
double	mCurrentHypoxicDuration
double	mCurrentHypoxiaOnsetTime
double	mHypoxicConcentration
double	mQuiescentConcentration
double	mCriticalHypoxicDuration
Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)
Friends
class	boost::serialization::access

Detailed Description

Simple oxygen-based cell-cycle model.

A simple oxygen-dependent cell-cycle model that inherits from AbstractSimpleCellCycleModel. The duration of G1 phase depends on the local oxygen concentration. A prolonged period of acute hypoxia leads to the cell being labelled as apoptotic. This model allows for quiescence imposed by transient periods of hypoxia, followed by reoxygenation.

Definition at line 51 of file SimpleOxygenBasedCellCycleModel.hpp.

Constructor & Destructor Documentation

SimpleOxygenBasedCellCycleModel::SimpleOxygenBasedCellCycleModel ( )

Constructor.

Definition at line 42 of file SimpleOxygenBasedCellCycleModel.cpp.

References SimulationTime::GetTime(), SimulationTime::Instance(), and mCurrentHypoxiaOnsetTime.

Referenced by CreateCellCycleModel().

Member Function Documentation

AbstractCellCycleModel * SimpleOxygenBasedCellCycleModel::CreateCellCycleModel ( ) [virtual]

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

Returns:: new cell-cycle model

Implements AbstractCellCycleModel.

Reimplemented in StochasticOxygenBasedCellCycleModel.

Definition at line 89 of file SimpleOxygenBasedCellCycleModel.cpp.

double SimpleOxygenBasedCellCycleModel::GetCriticalHypoxicDuration ( )

Returns:: mCriticalHypoxicDuration

Definition at line 185 of file SimpleOxygenBasedCellCycleModel.cpp.

References mCriticalHypoxicDuration.

double SimpleOxygenBasedCellCycleModel::GetCurrentHypoxiaOnsetTime ( )

Returns:: mCurrentHypoxiaOnsetTime

Definition at line 56 of file SimpleOxygenBasedCellCycleModel.cpp.

References mCurrentHypoxiaOnsetTime.

double SimpleOxygenBasedCellCycleModel::GetCurrentHypoxicDuration ( )

Returns:: mCurrentHypoxicDuration

Definition at line 51 of file SimpleOxygenBasedCellCycleModel.cpp.

References mCurrentHypoxicDuration.

double SimpleOxygenBasedCellCycleModel::GetHypoxicConcentration ( )

Returns:: mHypoxicConcentration

Definition at line 161 of file SimpleOxygenBasedCellCycleModel.cpp.

References mHypoxicConcentration.

double SimpleOxygenBasedCellCycleModel::GetQuiescentConcentration ( )

Returns:: mQuiescentConcentration

Definition at line 173 of file SimpleOxygenBasedCellCycleModel.cpp.

References mQuiescentConcentration.

void SimpleOxygenBasedCellCycleModel::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 AbstractSimpleCellCycleModel.

Reimplemented in StochasticOxygenBasedCellCycleModel.

Definition at line 202 of file SimpleOxygenBasedCellCycleModel.cpp.

References mCriticalHypoxicDuration, mHypoxicConcentration, and mQuiescentConcentration.

template<class Archive >

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

Boost Serialization method for archiving/checkpointing

Parameters:

	archive	The boost archive.
	version	The current version of this class.

Reimplemented from AbstractSimpleCellCycleModel.

Reimplemented in StochasticOxygenBasedCellCycleModel.

Definition at line 62 of file SimpleOxygenBasedCellCycleModel.hpp.

References mCriticalHypoxicDuration, mCurrentHypoxiaOnsetTime, mCurrentHypoxicDuration, mHypoxicConcentration, and mQuiescentConcentration.

void SimpleOxygenBasedCellCycleModel::SetCriticalHypoxicDuration ( double criticalHypoxicDuration )

Set method for mCriticalHypoxicDuration.

Parameters:

criticalHypoxicDuration

the new value of mCriticalHypoxicDuration

Definition at line 190 of file SimpleOxygenBasedCellCycleModel.cpp.

References mCriticalHypoxicDuration.

Referenced by StochasticOxygenBasedCellCycleModel::CreateCellCycleModel(), and CreateCellCycleModel().

void SimpleOxygenBasedCellCycleModel::SetCurrentHypoxiaOnsetTime ( double currentHypoxiaOnsetTime )

Set method for mCurrentHypoxiaOnsetTime.

Parameters:

currentHypoxiaOnsetTime

the new value of mCurrentHypoxiaOnsetTime

Definition at line 196 of file SimpleOxygenBasedCellCycleModel.cpp.

References mCurrentHypoxiaOnsetTime.

Referenced by StochasticOxygenBasedCellCycleModel::CreateCellCycleModel(), and CreateCellCycleModel().

void SimpleOxygenBasedCellCycleModel::SetHypoxicConcentration ( double hypoxicConcentration )

Set method for mHypoxicConcentration.

Parameters:

hypoxicConcentration

the new value of mHypoxicConcentration

Definition at line 166 of file SimpleOxygenBasedCellCycleModel.cpp.

References mHypoxicConcentration.

Referenced by StochasticOxygenBasedCellCycleModel::CreateCellCycleModel(), and CreateCellCycleModel().

void SimpleOxygenBasedCellCycleModel::SetQuiescentConcentration ( double quiescentConcentration )

Set method for mQuiescentConcentration.

Parameters:

quiescentConcentration

the new value of mQuiescentConcentration

Definition at line 178 of file SimpleOxygenBasedCellCycleModel.cpp.

References mQuiescentConcentration.

Referenced by StochasticOxygenBasedCellCycleModel::CreateCellCycleModel(), and CreateCellCycleModel().

void SimpleOxygenBasedCellCycleModel::UpdateCellCyclePhase ( ) [virtual]

Overridden UpdateCellCyclePhase() method.

Reimplemented from AbstractSimpleCellCycleModel.

Definition at line 61 of file SimpleOxygenBasedCellCycleModel.cpp.

References SimulationTime::GetTimeStep(), SimulationTime::Instance(), AbstractCellCycleModel::mCurrentCellCyclePhase, AbstractCellCycleModel::mG1Duration, AbstractCellCycleModel::mpCell, mQuiescentConcentration, and UpdateHypoxicDuration().

void SimpleOxygenBasedCellCycleModel::UpdateHypoxicDuration ( )

Method for updating mCurrentHypoxicDuration, called at the start of ReadyToDivide().

Definition at line 123 of file SimpleOxygenBasedCellCycleModel.cpp.

References SimulationTime::GetTime(), RandomNumberGenerator::Instance(), SimulationTime::Instance(), mCriticalHypoxicDuration, mCurrentHypoxiaOnsetTime, mCurrentHypoxicDuration, mHypoxicConcentration, AbstractCellCycleModel::mpCell, and RandomNumberGenerator::ranf().

Referenced by UpdateCellCyclePhase().

Friends And Related Function Documentation

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

Needed for serialization.

Reimplemented from AbstractSimpleCellCycleModel.

Reimplemented in StochasticOxygenBasedCellCycleModel.

Definition at line 55 of file SimpleOxygenBasedCellCycleModel.hpp.

Member Data Documentation

double SimpleOxygenBasedCellCycleModel::mCriticalHypoxicDuration [protected]

Non-dimensionalized critical hypoxic duration. Has units of hours.

Definition at line 103 of file SimpleOxygenBasedCellCycleModel.hpp.

Referenced by StochasticOxygenBasedCellCycleModel::CreateCellCycleModel(), CreateCellCycleModel(), GetCriticalHypoxicDuration(), OutputCellCycleModelParameters(), serialize(), SetCriticalHypoxicDuration(), and UpdateHypoxicDuration().

double SimpleOxygenBasedCellCycleModel::mCurrentHypoxiaOnsetTime [protected]

The time when the current period of hypoxia began.

Definition at line 83 of file SimpleOxygenBasedCellCycleModel.hpp.

Referenced by StochasticOxygenBasedCellCycleModel::CreateCellCycleModel(), CreateCellCycleModel(), GetCurrentHypoxiaOnsetTime(), serialize(), SetCurrentHypoxiaOnsetTime(), SimpleOxygenBasedCellCycleModel(), and UpdateHypoxicDuration().

double SimpleOxygenBasedCellCycleModel::mCurrentHypoxicDuration [protected]

How long the current period of hypoxia has lasted. Has units of hours.

Definition at line 78 of file SimpleOxygenBasedCellCycleModel.hpp.

Referenced by GetCurrentHypoxicDuration(), serialize(), and UpdateHypoxicDuration().

double SimpleOxygenBasedCellCycleModel::mHypoxicConcentration [protected]

Non-dimensionalized oxygen concentration below which cells are considered to be hypoxic. A prolonged period of hypoxia causes the cell to become apoptotic.

Definition at line 90 of file SimpleOxygenBasedCellCycleModel.hpp.

Referenced by StochasticOxygenBasedCellCycleModel::CreateCellCycleModel(), CreateCellCycleModel(), GetHypoxicConcentration(), OutputCellCycleModelParameters(), serialize(), SetHypoxicConcentration(), and UpdateHypoxicDuration().

double SimpleOxygenBasedCellCycleModel::mQuiescentConcentration [protected]

Non-dimensionalized oxygen concentration below which cells are considered to be quiescent and slow their progress through the G1 phase of the cell cycle.

Definition at line 97 of file SimpleOxygenBasedCellCycleModel.hpp.

Referenced by StochasticOxygenBasedCellCycleModel::CreateCellCycleModel(), CreateCellCycleModel(), GetQuiescentConcentration(), OutputCellCycleModelParameters(), serialize(), SetQuiescentConcentration(), and UpdateCellCyclePhase().

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

cell_based/src/population/cell/cycle/SimpleOxygenBasedCellCycleModel.hpp
cell_based/src/population/cell/cycle/SimpleOxygenBasedCellCycleModel.cpp

SimpleOxygenBasedCellCycleModel Class Reference

Public Member Functions

Protected Attributes

Private Member Functions

Friends

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation