#include <TysonNovak2001OdeSystem.hpp>

Inheritance diagram for TysonNovak2001OdeSystem:

Collaboration diagram for TysonNovak2001OdeSystem:

Public Member Functions
	TysonNovak2001OdeSystem (std::vector< double > stateVariables=std::vector< double >())

	~TysonNovak2001OdeSystem ()

void	Init ()

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

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

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

virtual void	AnalyticJacobian (const std::vector< double > &rSolutionGuess, double **jacobian, double time, double timeStep)

Public Member Functions inherited from AbstractOdeSystemWithAnalyticJacobian
	AbstractOdeSystemWithAnalyticJacobian (unsigned numberOfStateVariables=0)

Public Member Functions inherited from AbstractOdeSystem
	AbstractOdeSystem (unsigned numberOfStateVariables)

virtual	~AbstractOdeSystem ()

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	mK1

double	mK2d

double	mK2dd

double	mK2ddd

double	mCycB_threshold

double	mK3d

double	mK3dd

double	mK4d

double	mK4

double	mJ3

double	mJ4

double	mK5d

double	mK5dd

double	mK6

double	mJ5

unsigned	mN

double	mK7

double	mK8

double	mJ7

double	mJ8

double	mMad

double	mK9

double	mK10

double	mK11

double	mK12d

double	mK12dd

double	mK12ddd

double	mKeq

double	mK13

double	mK14

double	mK15d

double	mK15dd

double	mK16d

double	mK16dd

double	mJ15

double	mJ16

double	mMu

double	mMstar

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 Tyson & Novak (2001) system of ODEs. [doi:10.1006/jtbi.2001.2293]

Definition at line 51 of file TysonNovak2001OdeSystem.hpp.

Constructor & Destructor Documentation

TysonNovak2001OdeSystem::TysonNovak2001OdeSystem ( std::vector< double > stateVariables = std::vector<double>() )

Constructor.

Parameters

stateVariables optional initial conditions for state variables (only used in archiving)

Definition at line 40 of file TysonNovak2001OdeSystem.cpp.

References Init(), OdeSystemInformation< ODE_SYSTEM >::Instance(), AbstractUntemplatedParameterisedSystem::mpSystemInfo, and AbstractParameterisedSystem< std::vector< double > >::SetStateVariables().

Referenced by serialize().

TysonNovak2001OdeSystem::~TysonNovak2001OdeSystem ( )

Destructor.

Definition at line 53 of file TysonNovak2001OdeSystem.cpp.

Referenced by serialize().

Member Function Documentation

void TysonNovak2001OdeSystem::AnalyticJacobian	(	const std::vector< double > &	rSolutionGuess,
		double **	jacobian,
		double	time,
		double	timeStep
	)

virtual

Compute the Jacobian of the ODE system.

Parameters

rSolutionGuess	initial guess for the solution vector.
jacobian	the Jacobian of the ODE system.
time	at which to calculate the Jacobian.
timeStep	used to calculate the Jacobian.

Implements AbstractOdeSystemWithAnalyticJacobian.

Definition at line 161 of file TysonNovak2001OdeSystem.cpp.

References mJ3, mJ4, mJ5, mJ7, mJ8, mK10, mK2d, mK2dd, mK3d, mK3dd, mK4, mK5dd, mK6, mK7, mK8, mK9, mMad, mMstar, mMu, mN, and SmallPow().

Referenced by serialize().

double TysonNovak2001OdeSystem::CalculateRootFunction	(	double	time,
		const std::vector< double > &	rY
	)

virtual

Calculate whether the conditions for the cell cycle to finish have been met. (Used by CVODE solver to find exact stopping position)

Parameters

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

Returns: How close we are to the root of the stopping condition

Reimplemented from AbstractOdeSystem.

Definition at line 234 of file TysonNovak2001OdeSystem.cpp.

References EvaluateYDerivatives(), and mCycB_threshold.

Referenced by serialize().

bool TysonNovak2001OdeSystem::CalculateStoppingEvent	(	double	time,
		const std::vector< double > &	rY
	)

virtual

Calculate whether the conditions for the cell cycle to finish have been met. (Used by Chaste solvers to find whether or not to stop solving)

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 224 of file TysonNovak2001OdeSystem.cpp.

References EvaluateYDerivatives(), and mCycB_threshold.

Referenced by serialize().

void TysonNovak2001OdeSystem::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).

1. [CycB] 2. [Cdh1] 3. [Cdc20T] 4. [Cdc20A] 5. [IEP] 6. m - mass of the cell

Implements AbstractOdeSystem.

Definition at line 101 of file TysonNovak2001OdeSystem.cpp.

References mJ3, mJ4, mJ5, mJ7, mJ8, mK1, mK10, mK2d, mK2dd, mK3d, mK3dd, mK4, mK5d, mK5dd, mK6, mK7, mK8, mK9, mMad, mMstar, mMu, mN, and SmallPow().