Alarcon2004OxygenBasedCellCycleOdeSystem Class Reference

#include <Alarcon2004OxygenBasedCellCycleOdeSystem.hpp>

Inheritance diagram for Alarcon2004OxygenBasedCellCycleOdeSystem:

Collaboration diagram for Alarcon2004OxygenBasedCellCycleOdeSystem:

List of all members.

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

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

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 51 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

Todo:: should this be 0.004??

Definition at line 31 of file Alarcon2004OxygenBasedCellCycleOdeSystem.cpp.

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

Alarcon2004OxygenBasedCellCycleOdeSystem::~Alarcon2004OxygenBasedCellCycleOdeSystem ( )

Destructor.

Definition at line 78 of file Alarcon2004OxygenBasedCellCycleOdeSystem.cpp.

Member Function Documentation

template<class Archive>

void Alarcon2004OxygenBasedCellCycleOdeSystem::serialize	(	Archive &	archive,
		const unsigned int	version
	)			`[inline, private]`

Serialize the object and its member variables.

Parameters:

	archive	the archive
	version	the current version of this class

Definition at line 108 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

void Alarcon2004OxygenBasedCellCycleOdeSystem::Init ( )

Initialise parameter values.

Definition at line 83 of file Alarcon2004OxygenBasedCellCycleOdeSystem.cpp.

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

Referenced by Alarcon2004OxygenBasedCellCycleOdeSystem().

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 101 of file Alarcon2004OxygenBasedCellCycleOdeSystem.cpp.

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

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 150 of file Alarcon2004OxygenBasedCellCycleOdeSystem.cpp.

References mxThreshold, and myThreshold.

void Alarcon2004OxygenBasedCellCycleOdeSystem::SetIsLabelled ( bool isLabelled )

Set mIsLabelled.

Parameters:

isLabelled

whether the cell associated with this cell cycle ODE system is labelled (this affects the ODE system)

Definition at line 185 of file Alarcon2004OxygenBasedCellCycleOdeSystem.cpp.

References mIsLabelled.

bool Alarcon2004OxygenBasedCellCycleOdeSystem::IsLabelled ( ) const

Get method for mIsLabelled.

Definition at line 190 of file Alarcon2004OxygenBasedCellCycleOdeSystem.cpp.

References mIsLabelled.

double Alarcon2004OxygenBasedCellCycleOdeSystem::GetOxygenConcentration ( ) const

Get method for mOxygenConcentration.

Definition at line 195 of file Alarcon2004OxygenBasedCellCycleOdeSystem.cpp.

References mOxygenConcentration.

Member Data Documentation

double Alarcon2004OxygenBasedCellCycleOdeSystem::ma1 [private]

Constants for the Alarcon et al. (2004) model Dimensionless parameter a_1.

Definition at line 60 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by Alarcon2004OxygenBasedCellCycleOdeSystem(), and EvaluateYDerivatives().

double Alarcon2004OxygenBasedCellCycleOdeSystem::ma2 [private]

Dimensionless parameter a_2.

Definition at line 62 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double Alarcon2004OxygenBasedCellCycleOdeSystem::ma3 [private]

Dimensionless parameter a_3.

Definition at line 64 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double Alarcon2004OxygenBasedCellCycleOdeSystem::ma4 [private]

Dimensionless parameter a_4.

Definition at line 66 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double Alarcon2004OxygenBasedCellCycleOdeSystem::mb3 [private]

Dimensionless parameter b_3.

Definition at line 68 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double Alarcon2004OxygenBasedCellCycleOdeSystem::mb4 [private]

Dimensionless parameter b_4.

Definition at line 70 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double Alarcon2004OxygenBasedCellCycleOdeSystem::mc1 [private]

Dimensionless parameter c_1.

Definition at line 72 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by Alarcon2004OxygenBasedCellCycleOdeSystem(), and EvaluateYDerivatives().

double Alarcon2004OxygenBasedCellCycleOdeSystem::mc2 [private]

Dimensionless parameter c_2.

Definition at line 74 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double Alarcon2004OxygenBasedCellCycleOdeSystem::md1 [private]

Dimensionless parameter d_1.

Definition at line 76 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double Alarcon2004OxygenBasedCellCycleOdeSystem::md2 [private]

Dimensionless parameter d_2.

Definition at line 78 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double Alarcon2004OxygenBasedCellCycleOdeSystem::mJ3 [private]

Dimensionless parameter J_3.

Definition at line 80 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double Alarcon2004OxygenBasedCellCycleOdeSystem::mJ4 [private]

Dimensionless parameter J_4.

Definition at line 82 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double Alarcon2004OxygenBasedCellCycleOdeSystem::mEta [private]

Dimensionless parameter eta.

Definition at line 84 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double Alarcon2004OxygenBasedCellCycleOdeSystem::mMstar [private]

Dimensionless parameter m_star.

Definition at line 86 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by Alarcon2004OxygenBasedCellCycleOdeSystem(), EvaluateYDerivatives(), and Init().

double Alarcon2004OxygenBasedCellCycleOdeSystem::mB [private]

Dimensionless parameter B.

Definition at line 88 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double Alarcon2004OxygenBasedCellCycleOdeSystem::mxThreshold [private]

Dimensionless parameter x_THR.

Definition at line 90 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by Alarcon2004OxygenBasedCellCycleOdeSystem(), and CalculateStoppingEvent().

double Alarcon2004OxygenBasedCellCycleOdeSystem::myThreshold [private]

Dimensionless parameter y_THR.

Definition at line 92 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by Alarcon2004OxygenBasedCellCycleOdeSystem(), and CalculateStoppingEvent().

double Alarcon2004OxygenBasedCellCycleOdeSystem::mOxygenConcentration [private]

The oxygen concentration (this affects the ODE system).

Definition at line 95 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by GetOxygenConcentration().

bool Alarcon2004OxygenBasedCellCycleOdeSystem::mIsLabelled [private]

Whether the cell associated with this cell cycle ODE system is labelled (this affects the ODE system).

Definition at line 98 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Referenced by Alarcon2004OxygenBasedCellCycleOdeSystem(), EvaluateYDerivatives(), IsLabelled(), and SetIsLabelled().

The documentation for this class was generated from the following files:

cell_based/src/odes/Alarcon2004OxygenBasedCellCycleOdeSystem.hpp
cell_based/src/odes/Alarcon2004OxygenBasedCellCycleOdeSystem.cpp


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
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