#include <AbstractOdeBasedCellCycleModel.hpp>

Inheritance diagram for AbstractOdeBasedCellCycleModel:

Collaboration diagram for AbstractOdeBasedCellCycleModel:

Public Member Functions
	AbstractOdeBasedCellCycleModel (double lastTime=SimulationTime::Instance()->GetTime(), boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())
virtual	~AbstractOdeBasedCellCycleModel ()
virtual void	UpdateCellCyclePhase ()
double	GetOdeStopTime ()
void	SetBirthTime (double birthTime)
std::vector< double >	GetProteinConcentrations () const
void	SetProteinConcentrationsForTestsOnly (double lastTime, std::vector< double > proteinConcentrations)
virtual void	ResetForDivision ()
void	SetFinishedRunningOdes (bool finishedRunningOdes)
void	SetDivideTime (double divideTime)
void	SetG2PhaseStartTime (double g2PhaseStartTime)
virtual void	OutputCellCycleModelParameters (out_stream &rParamsFile)
Protected Attributes
double	mDivideTime
bool	mFinishedRunningOdes
double	mG2PhaseStartTime
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 standard cell cycle ODE models for intracellular protein concentrations (along the lines of Tyson & Novak), such as solving the ODEs until a stopping condition is met.

Definition at line 55 of file AbstractOdeBasedCellCycleModel.hpp.

Constructor & Destructor Documentation

AbstractOdeBasedCellCycleModel::AbstractOdeBasedCellCycleModel	(	double	lastTime = `SimulationTime::Instance()->GetTime()`,
		boost::shared_ptr< AbstractCellCycleModelOdeSolver >	pOdeSolver = `boost::shared_ptr<AbstractCellCycleModelOdeSolver>()`
	)

Creates an AbstractOdeBasedCellCycleModel, calls SetBirthTime on the AbstractCellCycleModel to make sure that can be set 'back in time' for cells which did not divide at the current time.

Parameters:

lastTime	The birth time of the cell / last time model was evaluated (defaults to the current SimulationTime)
pOdeSolver	An optional pointer to a cell-cycle model ODE solver object (allows the use of different ODE solvers)

Definition at line 41 of file AbstractOdeBasedCellCycleModel.cpp.

References SetBirthTime().

AbstractOdeBasedCellCycleModel::~AbstractOdeBasedCellCycleModel ( ) [virtual]

Destructor.

Definition at line 51 of file AbstractOdeBasedCellCycleModel.cpp.

Member Function Documentation

double AbstractOdeBasedCellCycleModel::GetOdeStopTime ( )

Get the time at which the ODE stopping event occurred. Only called in those subclasses for which stopping events are defined.

Returns:: the time at which the ODE system reached its stopping event

Definition at line 158 of file AbstractOdeBasedCellCycleModel.cpp.

References DOUBLE_UNSET, and CellCycleModelOdeHandler::mpOdeSolver.

Referenced by AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase(), and UpdateCellCyclePhase().

std::vector< double > AbstractOdeBasedCellCycleModel::GetProteinConcentrations ( ) const

Returns the protein concentrations at the current time (useful for tests)

NB: Will copy the vector - you can't use this to modify the concentrations.

Definition at line 62 of file AbstractOdeBasedCellCycleModel.cpp.

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

void AbstractOdeBasedCellCycleModel::OutputCellCycleModelParameters ( out_stream & rParamsFile ) [virtual]

Outputs cell cycle model parameters to file.

Parameters:

rParamsFile the file stream to which the parameters are output

Implements AbstractCellCycleModel.

Reimplemented in Alarcon2004OxygenBasedCellCycleModel, TysonNovakCellCycleModel, AbstractVanLeeuwen2009WntSwatCellCycleModel, AbstractWntOdeBasedCellCycleModel, StochasticWntCellCycleModel, VanLeeuwen2009WntSwatCellCycleModelHypothesisOne, VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo, and WntCellCycleModel.

Definition at line 183 of file AbstractOdeBasedCellCycleModel.cpp.

void AbstractOdeBasedCellCycleModel::ResetForDivision ( ) [virtual]

For a naturally cycling model this does not need to be overridden in the subclasses. But most models should override this function and then call AbstractOdeBasedCellCycleModel::ResetForDivision() from inside their version.

Reimplemented from AbstractCellCycleModel.

Reimplemented in Alarcon2004OxygenBasedCellCycleModel, TysonNovakCellCycleModel, AbstractWntOdeBasedCellCycleModel, and StochasticWntCellCycleModel.

Definition at line 147 of file AbstractOdeBasedCellCycleModel.cpp.

References AbstractCellCycleModel::mBirthTime, mDivideTime, mFinishedRunningOdes, AbstractCellCycleModel::mG1Duration, and CellCycleModelOdeHandler::mLastTime.

template<class Archive >

void AbstractOdeBasedCellCycleModel::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 AbstractCellCycleModel.

Reimplemented in Alarcon2004OxygenBasedCellCycleModel, TysonNovakCellCycleModel, AbstractVanLeeuwen2009WntSwatCellCycleModel, AbstractWntOdeBasedCellCycleModel, StochasticWntCellCycleModel, VanLeeuwen2009WntSwatCellCycleModelHypothesisOne, VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo, and WntCellCycleModel.

Definition at line 68 of file AbstractOdeBasedCellCycleModel.hpp.

References mDivideTime, mFinishedRunningOdes, and mG2PhaseStartTime.

void AbstractOdeBasedCellCycleModel::SetBirthTime ( double birthTime ) [virtual]

This overrides the AbstractCellCycleModel::SetBirthTime(double birthTime) because an ODE based cell-cycle model has more to reset...

Parameters:

birthTime the simulation time when the cell was born

Reimplemented from AbstractCellCycleModel.

Definition at line 55 of file AbstractOdeBasedCellCycleModel.cpp.

References mDivideTime, and CellCycleModelOdeHandler::mLastTime.

Referenced by AbstractOdeBasedCellCycleModel(), WntCellCycleModel::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), and Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel().

void AbstractOdeBasedCellCycleModel::SetDivideTime ( double divideTime )

Set mDivideTime.

Parameters:

divideTime the new value of mDivideTime

Definition at line 173 of file AbstractOdeBasedCellCycleModel.cpp.

References mDivideTime.

Referenced by WntCellCycleModel::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), and Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel().

void AbstractOdeBasedCellCycleModel::SetFinishedRunningOdes ( bool finishedRunningOdes )

Set mFinishedRunningOdes. Used in CreateCellCycleModel().

Parameters:

finishedRunningOdes the new value of mFinishedRunningOdes

Definition at line 168 of file AbstractOdeBasedCellCycleModel.cpp.

References mFinishedRunningOdes.

Referenced by WntCellCycleModel::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), and Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel().

void AbstractOdeBasedCellCycleModel::SetG2PhaseStartTime ( double g2PhaseStartTime )

Set mG2PhaseStartTime. Used in CreateCellCycleModel().

Parameters:

g2PhaseStartTime the new value of mG2PhaseStartTime

Definition at line 178 of file AbstractOdeBasedCellCycleModel.cpp.

References mG2PhaseStartTime.

Referenced by WntCellCycleModel::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), and Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel().

void AbstractOdeBasedCellCycleModel::SetProteinConcentrationsForTestsOnly	(	double	lastTime,
		std::vector< double >	proteinConcentrations
	)

Sets the protein concentrations and time when the model was last evaluated - should only be called by tests

Parameters:

lastTime	the SimulationTime at which the protein concentrations apply
proteinConcentrations	a standard vector of doubles of protein concentrations

Definition at line 68 of file AbstractOdeBasedCellCycleModel.cpp.

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

void AbstractOdeBasedCellCycleModel::UpdateCellCyclePhase ( ) [virtual]

Default UpdateCellCyclePhase() method for an ODE-based cell-cycle model. This method calls SolveOdeToTime() for G1 phase and adds time for the other phases.

Can be overridden if they should do something more subtle.

Implements AbstractCellCycleModel.

Reimplemented in AbstractWntOdeBasedCellCycleModel.

Definition at line 76 of file AbstractOdeBasedCellCycleModel.cpp.

References EXCEPTION, AbstractCellCycleModel::GetAge(), AbstractCellCycleModel::GetG2Duration(), AbstractCellCycleModel::GetMDuration(), AbstractUntemplatedParameterisedSystem::GetNumberOfStateVariables(), GetOdeStopTime(), AbstractCellCycleModel::GetSDuration(), SimulationTime::GetTime(), SimulationTime::Instance(), AbstractCellCycleModel::mBirthTime, AbstractCellCycleModel::mCurrentCellCyclePhase, mDivideTime, mFinishedRunningOdes, AbstractCellCycleModel::mG1Duration, mG2PhaseStartTime, CellCycleModelOdeHandler::mLastTime, CellCycleModelOdeHandler::mpOdeSystem, AbstractParameterisedSystem< VECTOR >::rGetStateVariables(), and CellCycleModelOdeHandler::SolveOdeToTime().