VanLeeuwen2009WntSwatCellCycleOdeSystem Class Reference

#include <VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp>

Inheritance diagram for VanLeeuwen2009WntSwatCellCycleOdeSystem:

Collaboration diagram for VanLeeuwen2009WntSwatCellCycleOdeSystem:

Public Member Functions
	VanLeeuwen2009WntSwatCellCycleOdeSystem (unsigned hypothesis, double wntLevel=0.0, boost::shared_ptr< AbstractCellMutationState > pMutationState=boost::shared_ptr< AbstractCellMutationState >(), std::vector< double > stateVariables=std::vector< double >())
	~VanLeeuwen2009WntSwatCellCycleOdeSystem ()
void	Init ()
void	SetMutationState (boost::shared_ptr< AbstractCellMutationState > pMutationState)
const boost::shared_ptr< AbstractCellMutationState >	GetMutationState () const
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)
double	GetWntLevel () const
unsigned	GetHypothesis () const
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	mk2d
double	mk3d
double	mk34d
double	mk43d
double	mk23d
double	mad
double	mJ11d
double	mJ12d
double	mJ13d
double	mJ61d
double	mJ62d
double	mJ63d
double	mKm1d
double	mkpd
double	mphi_r
double	mphi_i
double	mphi_j
double	mphi_p
double	mk16d
double	mk61d
double	mPhiE2F1
double	mSa
double	mSca
double	mSc
double	mSct
double	mSd
double	mSt
double	mSx
double	mSy
double	mDa
double	mDca
double	mDc
double	mDct
double	mDd
double	mDdx
double	mDt
double	mDu
double	mDx
double	mDy
double	mKc
double	mKd
double	mKt
double	mPc
double	mPu
double	mXiD
double	mXiDx
double	mXiX
double	mXiC
boost::shared_ptr< AbstractCellMutationState >	mpMutationState
unsigned	mHypothesis
double	mWntLevel

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 van Leeuwen et al. (2007) system of ODEs [doi:10.1016/j.jtbi.2007.01.019] coupled to the Swat et al. cell-cycle model equations. [doi:10.1093/bioinformatics/bth110]

The variables are

0. r = pRb 1. e = E2F1 (This is the S-phase indicator) 2. i = CycD (inactive) 3. j = CycD (active) 4. p = pRb-p 5. D = APC destruction complex 6. X = Axin 7. Cu = Beta Cat marked for ubiquitination 8. Co = Open form Beta Cat 9. Cc = Closed form Beta Cat 10. Mo = Open form Mutant Beta Cat 11. Mc = Closed form Mutant Beta Cat 12. A = Free Adhesion molecules 13. Ca = BetaCat/Adhesion 14. Ma = Mutant BetaCat/Adhesion 15. T = free TCF 16. Cot = Open BetaCat/TCF 17. Cct = Closed BetaCat/TCF 18. Mot = Open Mutant BetaCat/TCF 19. Mct = Closed Mutant BetaCat/TCF 20. Y = Wnt Target protein 21. Wnt level

Definition at line 81 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Constructor & Destructor Documentation

VanLeeuwen2009WntSwatCellCycleOdeSystem::VanLeeuwen2009WntSwatCellCycleOdeSystem	(	unsigned	hypothesis,
		double	wntLevel = 0.0,
		boost::shared_ptr< AbstractCellMutationState >	pMutationState = boost::shared_ptr<AbstractCellMutationState>(),
		std::vector< double >	stateVariables = std::vector<double>()
	)

Constructor.

Parameters

hypothesis	takes the value 1 or 2 and affects the ODE system.
wntLevel	is a non-dimensional Wnt value between 0 and 1. This sets up the Wnt pathway in its steady state.
pMutationState	cell mutation; some affect the ODE system
stateVariables	optional initial conditions for state variables (only used in archiving)

State variables are

0. r = pRb 1. e = E2F1 (This is the S-phase indicator) 2. i = CycD (inactive) 3. j = CycD (active) 4. p = pRb-p 5. D = APC destruction complex 6. X = Axin 7. Cu = Beta Cat marked for ubiquitination 8. Co = Open form Beta Cat 9. Cc = Closed form Beta Cat 10. Mo = Open form Mutant Beta Cat 11. Mc = Closed form Mutant Beta Cat 12. A = Free Adhesion molecules 13. Ca = BetaCat/Adhesion 14. Ma = Mutant BetaCat/Adhesion 15. T = free TCF 16. Cot = Open BetaCat/TCF 17. Cct = Closed BetaCat/TCF 18. Mot = Open Mutant BetaCat/TCF 19. Mct = Closed Mutant BetaCat/TCF 20. Y = Wnt Target protein 21. Wnt level

Definition at line 43 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.cpp.

References EXCEPTION, Init(), mDa, mDc, mDca, mDct, mDd, mDdx, mDt, mDu, mDx, mDy, mKc, mKd, mKt, mPc, mpMutationState, AbstractUntemplatedParameterisedSystem::mpSystemInfo, mPu, mSa, mSc, mSca, mSct, mSd, mSt, mSx, mSy, mXiC, mXiD, mXiDx, mXiX, AbstractParameterisedSystem< std::vector< double > >::SetDefaultInitialCondition(), AbstractParameterisedSystem< std::vector< double > >::SetStateVariables(), and SmallPow().

Referenced by serialize().

VanLeeuwen2009WntSwatCellCycleOdeSystem::~VanLeeuwen2009WntSwatCellCycleOdeSystem

(

)

Destructor.

Definition at line 163 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.cpp.

Referenced by serialize().

Member Function Documentation

double VanLeeuwen2009WntSwatCellCycleOdeSystem::CalculateRootFunction ( double  time, const std::vector< double > &  rY  )

virtual

When using CVODE this function is called instead of CalculateStoppingEvent. It allows the point at which rY[1] reaches 1 to be found to greater precision.

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 387 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.cpp.

Referenced by serialize().

bool VanLeeuwen2009WntSwatCellCycleOdeSystem::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 379 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.cpp.

References EvaluateYDerivatives().

Referenced by serialize().

void VanLeeuwen2009WntSwatCellCycleOdeSystem::EvaluateYDerivatives ( double  time, const std::vector< double > &  rY, std::vector< double > &  rDY  )

virtual

Compute the RHS of the 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 van Leeuwen et al. (2007) system of equations)

Implements AbstractOdeSystem.

Definition at line 259 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.cpp.

References mad, mDa, mDc, mDca, mDct, mDd, mDdx, mDt, mDu, mDx, mDy, mJ11d, mJ12d, mJ13d, mJ61d, mJ62d, mJ63d, mk16d, mk23d, mk2d, mk34d, mk3d, mk43d, mk61d, mKc, mKd, mKm1d, mkpd, mKt, mPc, mphi_i, mphi_j, mphi_p, mphi_r, mPhiE2F1, mpMutationState, mPu, mSa, mSc, mSca, mSct, mSd, mSt, mSx, mSy, mXiC, mXiD, mXiDx, and mXiX.

Referenced by CalculateStoppingEvent(), and serialize().

unsigned VanLeeuwen2009WntSwatCellCycleOdeSystem::GetHypothesis

(

)

const

Returns

mHypothesis.

Definition at line 491 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.cpp.

References CHASTE_CLASS_EXPORT, and mHypothesis.

Referenced by serialize().

const boost::shared_ptr< AbstractCellMutationState > VanLeeuwen2009WntSwatCellCycleOdeSystem::GetMutationState

(

)

const

Called by the archive function on the Wnt cell-cycle model.

Returns

mpMutationState the mutation state of the cell.

Definition at line 374 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.cpp.

References mpMutationState.

Referenced by serialize().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::GetWntLevel

(

)

const

Returns

mWntLevel.

Definition at line 486 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.cpp.

References mWntLevel.

Referenced by serialize().

void VanLeeuwen2009WntSwatCellCycleOdeSystem::Init

(

)

Initialise parameter values.

Definition at line 168 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.cpp.

References mad, mDa, mDc, mDca, mDct, mDd, mDdx, mDt, mDu, mDx, mDy, mHypothesis, mJ11d, mJ12d, mJ13d, mJ61d, mJ62d, mJ63d, mk16d, mk23d, mk2d, mk34d, mk3d, mk43d, mk61d, mKc, mKd, mKm1d, mkpd, mKt, mPc, mphi_i, mphi_j, mphi_p, mphi_r, mPhiE2F1, mPu, mSa, mSc, mSca, mSct, mSd, mSt, mSx, mSy, mXiC, mXiD, mXiDx, and mXiX.

Referenced by serialize(), and VanLeeuwen2009WntSwatCellCycleOdeSystem().

template<class Archive >

void VanLeeuwen2009WntSwatCellCycleOdeSystem::serialize ( Archive &  archive, const unsigned int  version  )

inlineprivate

Serialize the object and its member variables.

Parameters

archive	the archive
version	the current version of this class

Definition at line 212 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

References CalculateRootFunction(), CalculateStoppingEvent(), CHASTE_CLASS_EXPORT, EvaluateYDerivatives(), GetHypothesis(), GetMutationState(), GetWntLevel(), Init(), AbstractOdeSystem::rGetConstStateVariables(), SetMutationState(), VanLeeuwen2009WntSwatCellCycleOdeSystem(), and ~VanLeeuwen2009WntSwatCellCycleOdeSystem().

void VanLeeuwen2009WntSwatCellCycleOdeSystem::SetMutationState

(

boost::shared_ptr< AbstractCellMutationState >

pMutationState

)

Set the mutation state of the cell.

This should be called by the relevant cell-cycle model before any solving of the ODE system (as it is used to evaluate the Y derivatives).

Parameters

pMutationState

the mutation state.

Definition at line 158 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.cpp.

References mpMutationState.

Referenced by serialize().

Member Data Documentation

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mad

private

Dimensional parameter a.

Definition at line 100 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mDa

private

Dimensionless parameter d_A.

Definition at line 153 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), Init(), and VanLeeuwen2009WntSwatCellCycleOdeSystem().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mDc

private

Dimensionless parameter d_C.

Definition at line 157 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), Init(), and VanLeeuwen2009WntSwatCellCycleOdeSystem().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mDca

private

Dimensionless parameter d_CA.

Definition at line 155 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), Init(), and VanLeeuwen2009WntSwatCellCycleOdeSystem().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mDct

private

Dimensionless parameter d_CT.

Definition at line 159 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), Init(), and VanLeeuwen2009WntSwatCellCycleOdeSystem().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mDd

private

Dimensionless parameter d_D.

Definition at line 161 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), Init(), and VanLeeuwen2009WntSwatCellCycleOdeSystem().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mDdx

private

Dimensionless parameter d_Dx.

Definition at line 163 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), Init(), and VanLeeuwen2009WntSwatCellCycleOdeSystem().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mDt

private

Dimensionless parameter d_T.

Definition at line 165 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), Init(), and VanLeeuwen2009WntSwatCellCycleOdeSystem().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mDu

private

Dimensionless parameter d_U.

Definition at line 167 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), Init(), and VanLeeuwen2009WntSwatCellCycleOdeSystem().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mDx

private

Dimensionless parameter d_X.

Definition at line 169 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), Init(), and VanLeeuwen2009WntSwatCellCycleOdeSystem().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mDy

private

Dimensionless parameter d_Y.

Definition at line 171 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), Init(), and VanLeeuwen2009WntSwatCellCycleOdeSystem().

unsigned VanLeeuwen2009WntSwatCellCycleOdeSystem::mHypothesis

private

The hypothesis we are using = 1u for Van Leeuwen Hypothesis I = 2u for Van Leeuwen Hypothesis II

Definition at line 199 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by GetHypothesis(), and Init().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mJ11d

private

Dimensional parameter J_11.

Definition at line 102 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mJ12d

private

Dimensional parameter J_12.

Definition at line 104 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mJ13d

private

Dimensional parameter J_13.

Definition at line 106 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mJ61d

private

Dimensional parameter J_13.

Definition at line 108 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mJ62d

private

Dimensional parameter J_62.

Definition at line 110 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mJ63d

private

Dimensional parameter J_63.

Definition at line 112 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mk16d

private

Dimensional parameter k_16.

Definition at line 126 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mk23d

private

Dimensional parameter k_23.

Definition at line 98 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mk2d

private

Parameters for the Swat et al. (2004) modelDimensional parameter k_2.

Definition at line 90 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mk34d

private

Dimensional parameter k_34.

Definition at line 94 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mk3d

private

Dimensional parameter k_3.

Definition at line 92 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mk43d

private

Dimensional parameter k_2.

Definition at line 96 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mk61d

private

Dimensional parameter k_61.

Definition at line 128 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mKc

private

Dimensionless parameter K_c.

Definition at line 173 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), Init(), and VanLeeuwen2009WntSwatCellCycleOdeSystem().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mKd

private

Dimensionless parameter K_D.

Definition at line 175 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), Init(), and VanLeeuwen2009WntSwatCellCycleOdeSystem().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mKm1d

private

Dimensional parameter K_m1.

Definition at line 114 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mkpd

private

Dimensional parameter k_p.

Definition at line 116 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mKt

private

Dimensionless parameter K_T.

Definition at line 177 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), Init(), and VanLeeuwen2009WntSwatCellCycleOdeSystem().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mPc

private

Dimensionless parameter p_c.

Definition at line 179 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), Init(), and VanLeeuwen2009WntSwatCellCycleOdeSystem().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mphi_i

private

Dimensionless parameter phi_i.

Definition at line 120 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mphi_j

private

Dimensionless parameter phi_j.

Definition at line 122 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mphi_p

private

Dimensionless parameter phi_p.

Definition at line 124 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mphi_r

private

Dimensionless parameter phi_r.

Definition at line 118 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mPhiE2F1

private

Dimensionless parameter phi_E2F1.

Definition at line 130 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

boost::shared_ptr<AbstractCellMutationState> VanLeeuwen2009WntSwatCellCycleOdeSystem::mpMutationState

private

The mutation state of the cell.

Definition at line 192 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), GetMutationState(), SetMutationState(), and VanLeeuwen2009WntSwatCellCycleOdeSystem().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mPu

private

Dimensionless parameter p_u.

Definition at line 181 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), Init(), and VanLeeuwen2009WntSwatCellCycleOdeSystem().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mSa

private

Parameters for the Van Leeuwen et al. (2007) modelDimensionless parameter s_A.

Definition at line 137 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), Init(), and VanLeeuwen2009WntSwatCellCycleOdeSystem().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mSc

private

Dimensionless parameter s_C.

Definition at line 141 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), Init(), and VanLeeuwen2009WntSwatCellCycleOdeSystem().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mSca

private

Dimensionless parameter s_CA.

Definition at line 139 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), Init(), and VanLeeuwen2009WntSwatCellCycleOdeSystem().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mSct

private

Dimensionless parameter s_CT.

Definition at line 143 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), Init(), and VanLeeuwen2009WntSwatCellCycleOdeSystem().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mSd

private

Dimensionless parameter s_D.

Definition at line 145 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), Init(), and VanLeeuwen2009WntSwatCellCycleOdeSystem().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mSt

private

Dimensionless parameter s_T.

Definition at line 147 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), Init(), and VanLeeuwen2009WntSwatCellCycleOdeSystem().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mSx

private

Dimensionless parameter s_X.

Definition at line 149 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), Init(), and VanLeeuwen2009WntSwatCellCycleOdeSystem().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mSy

private

Dimensionless parameter s_Y.

Definition at line 151 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), Init(), and VanLeeuwen2009WntSwatCellCycleOdeSystem().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mWntLevel

private

The Wnt level (this affects the ODE system).

Definition at line 202 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by GetWntLevel().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mXiC

private

Dimensionless parameter xi_C.

Definition at line 189 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), Init(), and VanLeeuwen2009WntSwatCellCycleOdeSystem().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mXiD

private

Dimensionless parameter xi_D.

Definition at line 183 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), Init(), and VanLeeuwen2009WntSwatCellCycleOdeSystem().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mXiDx

private

Dimensionless parameter xi_Dx.

Definition at line 185 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), Init(), and VanLeeuwen2009WntSwatCellCycleOdeSystem().

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mXiX

private

Dimensionless parameter xi_X.

Definition at line 187 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), Init(), and VanLeeuwen2009WntSwatCellCycleOdeSystem().

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

• crypt/src/odes/VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp
• crypt/src/odes/VanLeeuwen2009WntSwatCellCycleOdeSystem.cpp