AbstractOdeBasedCellCycleModel Class Reference

#include <AbstractOdeBasedCellCycleModel.hpp>

Inherited by AbstractOdeBasedCellCycleModelWithStoppingEvent.

Collaboration diagram for AbstractOdeBasedCellCycleModel:

Public Member Functions
	AbstractOdeBasedCellCycleModel (double lastTime=SimulationTime::Instance()->GetTime())
	AbstractOdeBasedCellCycleModel (const AbstractOdeBasedCellCycleModel &rOtherModel)
virtual	~AbstractOdeBasedCellCycleModel ()
virtual void	UpdateCellCyclePhase ()
virtual bool	SolveOdeToTime (double currentTime)=0
virtual double	GetOdeStopTime ()=0
void	SetBirthTime (double birthTime)
std::vector< double >	GetProteinConcentrations () const
void	SetProteinConcentrationsForTestsOnly (double lastTime, std::vector< double > proteinConcentrations)
virtual void	ResetForDivision ()
Protected Attributes
AbstractOdeSystem *	mpOdeSystem
double	mLastTime
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 44 of file AbstractOdeBasedCellCycleModel.hpp.

Constructor & Destructor Documentation

AbstractOdeBasedCellCycleModel::AbstractOdeBasedCellCycleModel ( double lastTime = SimulationTime::Instance()->GetTime() )

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)

Definition at line 31 of file AbstractOdeBasedCellCycleModel.cpp.

References SetBirthTime().

AbstractOdeBasedCellCycleModel::AbstractOdeBasedCellCycleModel ( const AbstractOdeBasedCellCycleModel & rOtherModel )

Copy constructor.

This is needed because we store and manage a pointer to an ODE system. Note that this class doesn't actually copy the ODE system, because each subclass will use a different type. Hence subclasses *must* copy their own ODE system in their copy constructor.

Parameters:

rOtherModel

the cell cycle model being copied.

Definition at line 42 of file AbstractOdeBasedCellCycleModel.cpp.

AbstractOdeBasedCellCycleModel::~AbstractOdeBasedCellCycleModel ( ) [virtual]

This destructor deletes the mpOdeSystem.

Definition at line 53 of file AbstractOdeBasedCellCycleModel.cpp.

References mpOdeSystem.

Member Function Documentation

virtual double AbstractOdeBasedCellCycleModel::GetOdeStopTime ( ) [pure virtual]

This method must be implemented by each subclass

When the ODEs have reached a stopping event it returns the time at which the ODEs stopped running so a delay can be added in for S-G2-M phases if necessary.

Returns:: The time at which the ODE reached its stopping event.

Implemented in AbstractWntOdeBasedCellCycleModel, and TysonNovakCellCycleModel.

Referenced by 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 70 of file AbstractOdeBasedCellCycleModel.cpp.

References mpOdeSystem, and AbstractOdeSystem::rGetStateVariables().

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 AbstractWntOdeBasedCellCycleModel, StochasticWntCellCycleModel, and TysonNovakCellCycleModel.

Definition at line 158 of file AbstractOdeBasedCellCycleModel.cpp.

References AbstractCellCycleModel::mBirthTime, mDivideTime, mFinishedRunningOdes, AbstractCellCycleModel::mG1Duration, and 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 AbstractWntOdeBasedCellCycleModel, StochasticWntCellCycleModel, VanLeeuwen2009WntSwatCellCycleModelHypothesisOne, VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo, AbstractOdeBasedCellCycleModelWithStoppingEvent, and TysonNovakCellCycleModel.

Definition at line 57 of file AbstractOdeBasedCellCycleModel.hpp.

References mDivideTime, mFinishedRunningOdes, mG2PhaseStartTime, mLastTime, mpOdeSystem, and AbstractOdeSystem::rGetStateVariables().

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 62 of file AbstractOdeBasedCellCycleModel.cpp.

References mDivideTime, and mLastTime.

Referenced by AbstractOdeBasedCellCycleModel().

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 77 of file AbstractOdeBasedCellCycleModel.cpp.

References mLastTime, mpOdeSystem, AbstractOdeSystem::rGetStateVariables(), and AbstractOdeSystem::SetStateVariables().

virtual bool AbstractOdeBasedCellCycleModel::SolveOdeToTime ( double currentTime ) [pure virtual]

This method must be implemented by each subclass - solves the ODEs to a given time.

Parameters:

currentTime

the current time

Returns:: Whether a stopping event occurred.

Implemented in AbstractVanLeeuwen2009WntSwatCellCycleModel, WntCellCycleModel, and TysonNovakCellCycleModel.

Referenced by UpdateCellCyclePhase().

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.

Definition at line 86 of file AbstractOdeBasedCellCycleModel.cpp.

References AbstractCellCycleModel::GetAge(), AbstractCellCycleModel::GetG2Duration(), AbstractCellCycleModel::GetMDuration(), AbstractOdeSystem::GetNumberOfStateVariables(), GetOdeStopTime(), AbstractCellCycleModel::GetSDuration(), SimulationTime::GetTime(), SimulationTime::Instance(), AbstractCellCycleModel::mBirthTime, AbstractCellCycleModel::mCurrentCellCyclePhase, mDivideTime, mFinishedRunningOdes, AbstractCellCycleModel::mG1Duration, mG2PhaseStartTime, mLastTime, mpOdeSystem, AbstractOdeSystem::rGetStateVariables(), and SolveOdeToTime().