SingleOdeWntCellCycleModel Class Reference

#include <SingleOdeWntCellCycleModel.hpp>

Inheritance diagram for SingleOdeWntCellCycleModel:

Collaboration diagram for SingleOdeWntCellCycleModel:

List of all members.

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)

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

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 50 of file SingleOdeWntCellCycleModel.hpp.

Constructor & Destructor Documentation

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 32 of file SingleOdeWntCellCycleModel.cpp.

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

Referenced by CreateCellCycleModel().

Member Function Documentation

template<class Archive>

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

Archive the cell-cycle model and member variables.

Parameters:

	archive	the archive
	version	the current version of this class

Reimplemented from CellCycleModelOdeHandler.

Definition at line 63 of file SingleOdeWntCellCycleModel.hpp.

References mBetaCateninDivisionThreshold.

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 132 of file SingleOdeWntCellCycleModel.cpp.

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

Referenced by Initialise(), and UpdateCellCyclePhase().

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

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 123 of file SingleOdeWntCellCycleModel.cpp.

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

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 AbstractSimpleCellCycleModel.

Definition at line 103 of file SingleOdeWntCellCycleModel.cpp.

References ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel(), AbstractOdeSystem::GetInitialConditions(), SimpleWntCellCycleModel::GetWntLevel(), AbstractSimpleCellCycleModel::Initialise(), mBetaCateninDivisionThreshold, AbstractCellCycleModel::mBirthTime, AbstractCellCycleModel::mpCell, CellCycleModelOdeHandler::mpOdeSystem, CellCycleModelOdeHandler::SetLastTime(), and AbstractOdeSystem::SetStateVariables().

void SingleOdeWntCellCycleModel::UpdateCellCyclePhase ( ) [virtual]

This specialisation updates the beta-catenin level

Don't call the SimpleWntCellCycleModel - it will overwrite this.

Reimplemented from SimpleWntCellCycleModel.

Definition at line 95 of file SingleOdeWntCellCycleModel.cpp.

References ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel(), SimulationTime::Instance(), CellCycleModelOdeHandler::SolveOdeToTime(), and AbstractSimpleCellCycleModel::UpdateCellCyclePhase().

AbstractCellCycleModel * SingleOdeWntCellCycleModel::CreateCellCycleModel ( ) [virtual]

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

Reimplemented from SimpleWntCellCycleModel.

Definition at line 50 of file SingleOdeWntCellCycleModel.cpp.

double SingleOdeWntCellCycleModel::GetBetaCateninConcentration ( )

Return the total beta-catenin concentration

Definition at line 146 of file SingleOdeWntCellCycleModel.cpp.

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

Referenced by ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel().

void SingleOdeWntCellCycleModel::SetBetaCateninDivisionThreshold ( double betaCateninDivisionThreshold )

Set mBetaCateninDivisionThreshold.

Parameters:

betaCateninDivisionThreshold

to be set

Definition at line 151 of file SingleOdeWntCellCycleModel.cpp.

References mBetaCateninDivisionThreshold.

Referenced by CreateCellCycleModel().

double SingleOdeWntCellCycleModel::GetBetaCateninDivisionThreshold ( )

Get mBetaCateninDivisionThreshold.

Definition at line 156 of file SingleOdeWntCellCycleModel.cpp.

References mBetaCateninDivisionThreshold.

Referenced by ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel().

void SingleOdeWntCellCycleModel::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 SimpleWntCellCycleModel.

Definition at line 161 of file SingleOdeWntCellCycleModel.cpp.

References SimpleWntCellCycleModel::OutputCellCycleModelParameters().

Friends And Related Function Documentation

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

Needed for serialization.

Reimplemented from CellCycleModelOdeHandler.

Definition at line 55 of file SingleOdeWntCellCycleModel.hpp.

Member Data Documentation

double SingleOdeWntCellCycleModel::mBetaCateninDivisionThreshold [private]

The cell differentiates when the beta-catenin level drops below this value. It is hard coded in Initialise() because there are so many constructors.

Set and Get methods are also provided.

Definition at line 77 of file SingleOdeWntCellCycleModel.hpp.

Referenced by CreateCellCycleModel(), GetBetaCateninDivisionThreshold(), Initialise(), serialize(), and SetBetaCateninDivisionThreshold().

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

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


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)
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