#include <TysonNovakCellCycleModel.hpp>

Inheritance diagram for TysonNovakCellCycleModel:

Collaboration diagram for TysonNovakCellCycleModel:

Public Member Functions
	TysonNovakCellCycleModel (boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())
void	Initialise ()
void	ResetForDivision ()
AbstractCellCycleModel *	CreateCellCycleModel ()
double	GetSDuration ()
double	GetG2Duration ()
double	GetMDuration ()
void	InitialiseDaughterCell ()
double	GetAverageTransitCellCycleTime ()
double	GetAverageStemCellCycleTime ()
bool	CanCellTerminallyDifferentiate ()
virtual void	OutputCellCycleModelParameters (out_stream &rParamsFile)
Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)
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 55 of file TysonNovakCellCycleModel.hpp.

Constructor & Destructor Documentation

TysonNovakCellCycleModel::TysonNovakCellCycleModel ( 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 TysonNovakCellCycleModel.cpp.

References CellCycleModelOdeHandler::mpOdeSolver, and CellCycleModelOdeHandler::SetDt().

Referenced by CreateCellCycleModel().

Member Function Documentation

bool TysonNovakCellCycleModel::CanCellTerminallyDifferentiate ( ) [virtual]

Overridden CanCellTerminallyDifferentiate() method.

Reimplemented from AbstractCellCycleModel.

Definition at line 186 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 101 of file TysonNovakCellCycleModel.cpp.

double TysonNovakCellCycleModel::GetAverageStemCellCycleTime ( ) [virtual]

Overridden GetAverageStemCellCycleTime() method.

Reimplemented from AbstractCellCycleModel.

Definition at line 181 of file TysonNovakCellCycleModel.cpp.

double TysonNovakCellCycleModel::GetAverageTransitCellCycleTime ( ) [virtual]

Overridden GetAverageTransitCellCycleTime() method.

Reimplemented from AbstractCellCycleModel.

Definition at line 176 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 156 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 166 of file TysonNovakCellCycleModel.cpp.

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 146 of file TysonNovakCellCycleModel.cpp.

void TysonNovakCellCycleModel::Initialise ( void ) [virtual]

Initialise the cell-cycle model at the start of a simulation.

This method will be called precisely once per cell set up in the initial cell population. It is not called on cell division; use ResetForDivision(), CreateCellCycleModel() and InitialiseDaughterCell() for that.

By the time this is called, a CellPopulation will have been set up, so the model can know where its cell is located in space. If relevant to the simulation, any singletons will also have been initialised.

Reimplemented from AbstractCellCycleModel.

Definition at line 59 of file TysonNovakCellCycleModel.cpp.

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

void TysonNovakCellCycleModel::InitialiseDaughterCell ( ) [virtual]

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

Reimplemented from AbstractCellCycleModel.

Definition at line 93 of file TysonNovakCellCycleModel.cpp.

References AbstractCellCycleModel::mpCell.

void TysonNovakCellCycleModel::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.

Definition at line 191 of file TysonNovakCellCycleModel.cpp.

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 68 of file TysonNovakCellCycleModel.cpp.

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

template<class Archive >