#include <Alarcon2004OxygenBasedCellCycleOdeSystem.hpp>

Inheritance diagram for Alarcon2004OxygenBasedCellCycleOdeSystem:

Collaboration diagram for Alarcon2004OxygenBasedCellCycleOdeSystem:

Public Member Functions
	Alarcon2004OxygenBasedCellCycleOdeSystem (double oxygenConcentration, bool isLabelled, std::vector< double > stateVariables=std::vector< double >())

	~Alarcon2004OxygenBasedCellCycleOdeSystem ()

void	Init ()

void	EvaluateYDerivatives (double time, const std::vector< double > &rY, std::vector< double > &rDY)

bool	CalculateStoppingEvent (double time, const std::vector< double > &rY)

void	SetIsLabelled (bool isLabelled)

bool	IsLabelled () const

double	GetOxygenConcentration () const

Public Member Functions inherited from AbstractOdeSystem
	AbstractOdeSystem (unsigned numberOfStateVariables)

virtual	~AbstractOdeSystem ()

virtual double	CalculateRootFunction (double time, const std::vector< double > &rY)

bool	GetUseAnalyticJacobian ()

const std::vector< double > &	rGetConstStateVariables () const

Public Member Functions inherited from AbstractParameterisedSystem< std::vector< double > >
	AbstractParameterisedSystem (unsigned numberOfStateVariables)

std::vector< double > &	rGetStateVariables ()

std::vector< double >	GetStateVariables ()

void	SetStateVariables (const std::vector< double > &rStateVariables)

double	GetStateVariable (unsigned index) const

double	GetStateVariable (const std::string &rName) const

void	SetStateVariable (unsigned index, double newValue)

void	SetStateVariable (const std::string &rName, double newValue)

virtual void	VerifyStateVariables ()

void	SetDefaultInitialConditions (const std::vector< double > &rInitialConditions)

void	SetDefaultInitialCondition (unsigned index, double initialCondition)

std::vector< double >	GetInitialConditions () const

void	ResetToInitialConditions ()

double	GetParameter (unsigned index) const

double	GetParameter (const std::string &rName) const

void	SetParameter (const std::string &rName, double value)

void	SetParameter (unsigned index, double value)

double	GetAnyVariable (unsigned index, double time=0.0, std::vector< double > *pDerivedQuantities=NULL)

double	GetAnyVariable (const std::string &rName, double time=0.0, std::vector< double > *pDerivedQuantities=NULL)

void	SetAnyVariable (unsigned index, double value)

void	SetAnyVariable (const std::string &rName, double value)

virtual std::vector< double >	ComputeDerivedQuantities (double time, const std::vector< double > &rState)

std::vector< double >	ComputeDerivedQuantitiesFromCurrentState (double time)

Public Member Functions inherited from AbstractUntemplatedParameterisedSystem
	AbstractUntemplatedParameterisedSystem (unsigned numberOfStateVariables)

virtual	~AbstractUntemplatedParameterisedSystem ()

boost::shared_ptr< const AbstractOdeSystemInformation >	GetSystemInformation () const

std::string	GetSystemName () const

unsigned	GetNumberOfAttributes () const

bool	HasAttribute (const std::string &rName) const

double	GetAttribute (const std::string &rName) const

unsigned	GetNumberOfStateVariables () const

const std::vector< std::string > &	rGetStateVariableNames () const

const std::vector< std::string > &	rGetStateVariableUnits () const

unsigned	GetStateVariableIndex (const std::string &rName) const

bool	HasStateVariable (const std::string &rName) const

std::string	GetStateVariableUnits (unsigned index) const

unsigned	GetNumberOfParameters () const

const std::vector< std::string > &	rGetParameterNames () const

const std::vector< std::string > &	rGetParameterUnits () const

unsigned	GetParameterIndex (const std::string &rName) const

bool	HasParameter (const std::string &rName) const

std::string	GetParameterUnits (unsigned index) const

unsigned	GetNumberOfDerivedQuantities () const

const std::vector< std::string > &	rGetDerivedQuantityNames () const

const std::vector< std::string > &	rGetDerivedQuantityUnits () const

unsigned	GetDerivedQuantityIndex (const std::string &rName) const

bool	HasDerivedQuantity (const std::string &rName) const

std::string	GetDerivedQuantityUnits (unsigned index) const

unsigned	GetAnyVariableIndex (const std::string &rName) const

bool	HasAnyVariable (const std::string &rName) const

std::string	GetAnyVariableUnits (unsigned index) const

std::string	GetAnyVariableUnits (const std::string &rName) const

Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)

Private Attributes
double	ma1

double	ma2

double	ma3

double	ma4

double	mb3

double	mb4

double	mc1

double	mc2

double	md1

double	md2

double	mJ3

double	mJ4

double	mEta

double	mMstar

double	mB

double	mxThreshold

double	myThreshold

double	mOxygenConcentration

bool	mIsLabelled

Friends
class	boost::serialization::access

Additional Inherited Members
Protected Member Functions inherited from AbstractParameterisedSystem< std::vector< double > >
std::string	DumpState (const std::string &rMessage)

std::string	DumpState (const std::string &rMessage, std::vector< double >Y)

std::string	DumpState (const std::string &rMessage, std::vector< double >Y, double time)

void	CheckParametersOnLoad (const std::vector< double > &rParameters, const std::vector< std::string > &rParameterNames)

Protected Attributes inherited from AbstractOdeSystem
bool	mUseAnalyticJacobian

Protected Attributes inherited from AbstractParameterisedSystem< std::vector< double > >
std::vector< double >	mStateVariables

std::vector< double >	mParameters

Protected Attributes inherited from AbstractUntemplatedParameterisedSystem
unsigned	mNumberOfStateVariables

boost::shared_ptr < AbstractOdeSystemInformation >	mpSystemInfo

Detailed Description

Represents the Alarcon et al. (2004) system of ODEs (see ticket #461). [doi:10.1016/j.jtbi.2004.04.016]

The variables are

0. x = Cdh1-APC complexes 1. y = cyclin-CDK 2. z = p27 3. m = mass 4. u = RBNP 5. P = oxygen concentration

Definition at line 59 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Constructor & Destructor Documentation

Alarcon2004OxygenBasedCellCycleOdeSystem::Alarcon2004OxygenBasedCellCycleOdeSystem	(	double	oxygenConcentration,
		bool	isLabelled,
		std::vector< double >	stateVariables = `std::vector<double>()`
	)

Constructor.

Parameters

oxygenConcentration	is a non-dimensional oxygen concentration value between 0 and 1
isLabelled	whether the cell associated with this cell cycle ODE system is labelled (this affects the ODE system)
stateVariables	optional initial conditions for state variables (only used in archiving)

State variables

0. x = Cdh1-APC complexes 1. y = cyclin-CDK 2. z = p27 3. m = mass 4. u = RBNP 5. oxygenConcentration

Definition at line 40 of file Alarcon2004OxygenBasedCellCycleOdeSystem.cpp.

References Init(), ma1, mc1, mIsLabelled, mMstar, AbstractUntemplatedParameterisedSystem::mpSystemInfo, mxThreshold, myThreshold, AbstractParameterisedSystem< std::vector< double > >::SetDefaultInitialCondition(), and AbstractParameterisedSystem< std::vector< double > >::SetStateVariables().

Alarcon2004OxygenBasedCellCycleOdeSystem::~Alarcon2004OxygenBasedCellCycleOdeSystem ( )

Destructor.

Definition at line 87 of file Alarcon2004OxygenBasedCellCycleOdeSystem.cpp.

Member Function Documentation

bool Alarcon2004OxygenBasedCellCycleOdeSystem::CalculateStoppingEvent	(	double	time,
		const std::vector< double > &	rY
	)

virtual

Calculate whether the conditions for the cell cycle to finish have been met.

Parameters

time	at which to calculate whether the stopping event has occurred
rY	value of the solution vector used to evaluate the RHS.

Returns: whether or not stopping conditions have been met

Reimplemented from AbstractOdeSystem.

Definition at line 159 of file Alarcon2004OxygenBasedCellCycleOdeSystem.cpp.

References mxThreshold, and myThreshold.

void Alarcon2004OxygenBasedCellCycleOdeSystem::EvaluateYDerivatives	(	double	time,
		const std::vector< double > &	rY,
		std::vector< double > &	rDY
	)

virtual

Compute the RHS of the Alarcon et al. (2004) system of ODEs.

Returns a vector representing the RHS of the ODEs at each time step, y' = [y1' ... yn']. An ODE solver will call this function repeatedly to solve for y = [y1 ... yn].

Parameters

time	used to evaluate the RHS.
rY	value of the solution vector used to evaluate the RHS.
rDY	filled in with the resulting derivatives (using Alarcons et al. (2004) system of equations).

Implements AbstractOdeSystem.

Definition at line 110 of file Alarcon2004OxygenBasedCellCycleOdeSystem.cpp.

References ma1, ma2, ma3, ma4, mB, mb3, mb4, mc1, mc2, md1, md2, mEta, mIsLabelled, mJ3, mJ4, and mMstar.