TysonNovakCellCycleModel Class Reference

#include <TysonNovakCellCycleModel.hpp>

Inherits AbstractOdeBasedCellCycleModelWithStoppingEvent.

Collaboration diagram for TysonNovakCellCycleModel:

Public Member Functions
	TysonNovakCellCycleModel ()
	TysonNovakCellCycleModel (const TysonNovakCellCycleModel &rOtherModel)
void	ResetForDivision ()
AbstractCellCycleModel *	CreateCellCycleModel ()
bool	SolveOdeToTime (double currentTime)
double	GetOdeStopTime ()
double	GetSDuration ()
double	GetG2Duration ()
double	GetMDuration ()
void	InitialiseDaughterCell ()
double	GetAverageTransitCellCycleTime ()
double	GetAverageStemCellCycleTime ()
virtual bool	CanCellTerminallyDifferentiate ()
Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)
Static Private Attributes
static BackwardEulerIvpOdeSolver	msSolver
Friends
class	TestOdeBasedCellCycleModels
class	boost::serialization::access

Detailed Description

Tyson-Novak 2001 cell cycle model, taken from the version at doi:10.1006/jtbi.2001.2293

Note that this is not a model for murine or human colonic-cell cycling, but is included in chaste as one of the most commonly known ODE based cell cycle models.

Time taken to progress through the cycle is deterministic and given by an ODE system independent of external factors.

Definition at line 50 of file TysonNovakCellCycleModel.hpp.

Constructor & Destructor Documentation

TysonNovakCellCycleModel::TysonNovakCellCycleModel ( )

Default constructor.

Definition at line 36 of file TysonNovakCellCycleModel.cpp.

References AbstractOdeSystem::GetInitialConditions(), AbstractOdeBasedCellCycleModel::mpOdeSystem, msSolver, and AbstractOdeSystem::SetStateVariables().

Referenced by CreateCellCycleModel().

TysonNovakCellCycleModel::TysonNovakCellCycleModel ( const TysonNovakCellCycleModel & rOtherModel )

Copy constructor.

Also creates a copy of our ODE system.

Parameters:

rOtherModel

the instance being copied.

Definition at line 47 of file TysonNovakCellCycleModel.cpp.

References AbstractOdeBasedCellCycleModel::mpOdeSystem.

Member Function Documentation

bool TysonNovakCellCycleModel::CanCellTerminallyDifferentiate ( ) [virtual]

Overridden CanCellTerminallyDifferentiate() method.

Reimplemented from AbstractCellCycleModel.

Definition at line 150 of file TysonNovakCellCycleModel.cpp.

AbstractCellCycleModel * TysonNovakCellCycleModel::CreateCellCycleModel ( ) [virtual]

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

Implements AbstractCellCycleModel.

Definition at line 89 of file TysonNovakCellCycleModel.cpp.

References TysonNovakCellCycleModel().

double TysonNovakCellCycleModel::GetAverageStemCellCycleTime ( ) [virtual]

Overridden GetAverageStemCellCycleTime() method.

Reimplemented from AbstractCellCycleModel.

Definition at line 144 of file TysonNovakCellCycleModel.cpp.

double TysonNovakCellCycleModel::GetAverageTransitCellCycleTime ( ) [virtual]

Overridden GetAverageTransitCellCycleTime() method.

Reimplemented from AbstractCellCycleModel.

Definition at line 139 of file TysonNovakCellCycleModel.cpp.

double TysonNovakCellCycleModel::GetG2Duration ( ) [virtual]

Get the duration of the cell's G2 phase.

Tyson & Novak pretends it is running ODEs in just G1, but they really represent the whole cell cycle so we set the other phases to zero.

Reimplemented from AbstractCellCycleModel.

Definition at line 119 of file TysonNovakCellCycleModel.cpp.

double TysonNovakCellCycleModel::GetMDuration ( ) [virtual]

Get the duration of the cell's M phase.

Tyson & Novak pretends it is running ODEs in just G1, but they really represent the whole cell cycle so we set the other phases to zero.

Reimplemented from AbstractCellCycleModel.

Definition at line 129 of file TysonNovakCellCycleModel.cpp.

double TysonNovakCellCycleModel::GetOdeStopTime ( ) [virtual]

Get the time at which the ODE stopping event occured.

Returns:: the stopping event time

Implements AbstractOdeBasedCellCycleModel.

Definition at line 103 of file TysonNovakCellCycleModel.cpp.

References AbstractIvpOdeSolver::GetStoppingTime(), msSolver, and AbstractIvpOdeSolver::StoppingEventOccurred().

double TysonNovakCellCycleModel::GetSDuration ( ) [virtual]

Get the duration of the cell's S phase.

Tyson & Novak pretends it is running ODEs in just G1, but they really represent the whole cell cycle, so we set the other phases to zero.

Reimplemented from AbstractCellCycleModel.

Definition at line 109 of file TysonNovakCellCycleModel.cpp.

void TysonNovakCellCycleModel::InitialiseDaughterCell ( ) [virtual]

If the daughter cell type is stem, change it to transit.

Reimplemented from AbstractCellCycleModel.

Definition at line 81 of file TysonNovakCellCycleModel.cpp.

References TissueCell::GetCellProliferativeType(), AbstractCellCycleModel::mpCell, and TissueCell::SetCellProliferativeType().

void TysonNovakCellCycleModel::ResetForDivision ( ) [virtual]

Reset cell cycle model by calling AbstractOdeBasedCellCycleModelWithStoppingEvent::ResetForDivision() and setting initial conditions for protein concentrations.

This model needs the protein concentrations and phase resetting to G0/G1.

In theory, the solution to the Tyson-Novak equations should exhibit stable oscillations, and we only need to halve the mass of the cell each period.

However, the backward Euler solver used to solve the equations currently returns a solution that diverges after long times, so we must reset the initial conditions each period.

When running with CVODE however we can use the halving the mass of the cell method.

Reimplemented from AbstractOdeBasedCellCycleModel.

Definition at line 56 of file TysonNovakCellCycleModel.cpp.

References AbstractOdeSystem::GetInitialConditions(), AbstractOdeBasedCellCycleModel::mpOdeSystem, AbstractOdeSystem::rGetStateVariables(), and AbstractOdeSystem::SetStateVariables().

template<class Archive >