Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
Public Member Functions | Private Member Functions | Private Attributes | Friends | List of all members
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::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
hypothesistakes the value 1 or 2 and affects the ODE system.
wntLevelis a non-dimensional Wnt value between 0 and 1. This sets up the Wnt pathway in its steady state.
pMutationStatecell mutation; some affect the ODE system
stateVariablesoptional 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 42 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(), and AbstractParameterisedSystem< std::vector< double > >::SetStateVariables().

◆ ~VanLeeuwen2009WntSwatCellCycleOdeSystem()

VanLeeuwen2009WntSwatCellCycleOdeSystem::~VanLeeuwen2009WntSwatCellCycleOdeSystem ( )

Destructor.

Definition at line 162 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.cpp.

Member Function Documentation

◆ CalculateRootFunction()

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
timeat which to calculate whether the stopping event has occurred
rYvalue 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 386 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.cpp.

◆ CalculateStoppingEvent()

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
timeat which to calculate whether the stopping event has occurred
rYvalue of the solution vector used to evaluate the RHS
Returns
whether or not stopping conditions have been met

Reimplemented from AbstractOdeSystem.

Definition at line 378 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.cpp.

References EvaluateYDerivatives().

◆ EvaluateYDerivatives()

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
timeused to evaluate the RHS.
rYvalue of the solution vector used to evaluate the RHS.
rDYfilled in with the resulting derivatives (using van Leeuwen et al. (2007) system of equations)

Implements AbstractOdeSystem.

Definition at line 258 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().

◆ GetHypothesis()

unsigned VanLeeuwen2009WntSwatCellCycleOdeSystem::GetHypothesis ( ) const
Returns
mHypothesis.

Definition at line 490 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.cpp.

References mHypothesis.

◆ GetMutationState()

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 373 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.cpp.

References mpMutationState.

◆ GetWntLevel()

double VanLeeuwen2009WntSwatCellCycleOdeSystem::GetWntLevel ( ) const
Returns
mWntLevel.

Definition at line 485 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.cpp.

References mWntLevel.

◆ Init()

void VanLeeuwen2009WntSwatCellCycleOdeSystem::Init ( )

Initialise parameter values.

Definition at line 167 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 VanLeeuwen2009WntSwatCellCycleOdeSystem().

◆ serialize()

template<class Archive >
void VanLeeuwen2009WntSwatCellCycleOdeSystem::serialize ( Archive &  archive,
const unsigned int  version 
)
inlineprivate

Serialize the object and its member variables.

Parameters
archivethe archive
versionthe current version of this class

Definition at line 212 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

◆ SetMutationState()

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
pMutationStatethe mutation state.

Definition at line 157 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.cpp.

References mpMutationState.

Friends And Related Symbol Documentation

◆ boost::serialization::access

friend class boost::serialization::access
friend

Definition at line 204 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Member Data Documentation

◆ mad

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mad
private

Dimensional parameter a.

Definition at line 100 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

◆ mDa

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mDa
private

Dimensionless parameter d_A.

Definition at line 153 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

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

◆ mDc

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mDc
private

Dimensionless parameter d_C.

Definition at line 157 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

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

◆ mDca

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mDca
private

Dimensionless parameter d_CA.

Definition at line 155 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

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

◆ mDct

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mDct
private

Dimensionless parameter d_CT.

Definition at line 159 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

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

◆ mDd

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mDd
private

Dimensionless parameter d_D.

Definition at line 161 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

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

◆ mDdx

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mDdx
private

Dimensionless parameter d_Dx.

Definition at line 163 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

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

◆ mDt

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mDt
private

Dimensionless parameter d_T.

Definition at line 165 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

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

◆ mDu

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mDu
private

Dimensionless parameter d_U.

Definition at line 167 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

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

◆ mDx

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mDx
private

Dimensionless parameter d_X.

Definition at line 169 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

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

◆ mDy

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mDy
private

Dimensionless parameter d_Y.

Definition at line 171 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

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

◆ mHypothesis

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().

◆ mJ11d

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mJ11d
private

Dimensional parameter J_11.

Definition at line 102 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

◆ mJ12d

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mJ12d
private

Dimensional parameter J_12.

Definition at line 104 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

◆ mJ13d

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mJ13d
private

Dimensional parameter J_13.

Definition at line 106 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

◆ mJ61d

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mJ61d
private

Dimensional parameter J_13.

Definition at line 108 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

◆ mJ62d

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mJ62d
private

Dimensional parameter J_62.

Definition at line 110 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

◆ mJ63d

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mJ63d
private

Dimensional parameter J_63.

Definition at line 112 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

◆ mk16d

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mk16d
private

Dimensional parameter k_16.

Definition at line 126 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

◆ mk23d

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mk23d
private

Dimensional parameter k_23.

Definition at line 98 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

◆ mk2d

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mk2d
private

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

Definition at line 90 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

◆ mk34d

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mk34d
private

Dimensional parameter k_34.

Definition at line 94 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

◆ mk3d

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mk3d
private

Dimensional parameter k_3.

Definition at line 92 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

◆ mk43d

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mk43d
private

Dimensional parameter k_2.

Definition at line 96 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

◆ mk61d

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mk61d
private

Dimensional parameter k_61.

Definition at line 128 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

◆ mKc

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mKc
private

Dimensionless parameter K_c.

Definition at line 173 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

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

◆ mKd

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mKd
private

Dimensionless parameter K_D.

Definition at line 175 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

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

◆ mKm1d

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mKm1d
private

Dimensional parameter K_m1.

Definition at line 114 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

◆ mkpd

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mkpd
private

Dimensional parameter k_p.

Definition at line 116 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

◆ mKt

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mKt
private

Dimensionless parameter K_T.

Definition at line 177 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

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

◆ mPc

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mPc
private

Dimensionless parameter p_c.

Definition at line 179 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

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

◆ mphi_i

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mphi_i
private

Dimensionless parameter phi_i.

Definition at line 120 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

◆ mphi_j

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mphi_j
private

Dimensionless parameter phi_j.

Definition at line 122 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

◆ mphi_p

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mphi_p
private

Dimensionless parameter phi_p.

Definition at line 124 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

◆ mphi_r

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mphi_r
private

Dimensionless parameter phi_r.

Definition at line 118 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

◆ mPhiE2F1

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mPhiE2F1
private

Dimensionless parameter phi_E2F1.

Definition at line 130 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

◆ mpMutationState

boost::shared_ptr<AbstractCellMutationState> VanLeeuwen2009WntSwatCellCycleOdeSystem::mpMutationState
private

The mutation state of the cell.

Definition at line 192 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

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

◆ mPu

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mPu
private

Dimensionless parameter p_u.

Definition at line 181 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

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

◆ mSa

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mSa
private

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

Definition at line 137 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

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

◆ mSc

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mSc
private

Dimensionless parameter s_C.

Definition at line 141 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

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

◆ mSca

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mSca
private

Dimensionless parameter s_CA.

Definition at line 139 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

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

◆ mSct

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mSct
private

Dimensionless parameter s_CT.

Definition at line 143 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

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

◆ mSd

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mSd
private

Dimensionless parameter s_D.

Definition at line 145 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

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

◆ mSt

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mSt
private

Dimensionless parameter s_T.

Definition at line 147 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

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

◆ mSx

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mSx
private

Dimensionless parameter s_X.

Definition at line 149 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

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

◆ mSy

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mSy
private

Dimensionless parameter s_Y.

Definition at line 151 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

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

◆ mWntLevel

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mWntLevel
private

The Wnt level (this affects the ODE system).

Definition at line 202 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

Referenced by GetWntLevel().

◆ mXiC

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mXiC
private

Dimensionless parameter xi_C.

Definition at line 189 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

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

◆ mXiD

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mXiD
private

Dimensionless parameter xi_D.

Definition at line 183 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

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

◆ mXiDx

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mXiDx
private

Dimensionless parameter xi_Dx.

Definition at line 185 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

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

◆ mXiX

double VanLeeuwen2009WntSwatCellCycleOdeSystem::mXiX
private

Dimensionless parameter xi_X.

Definition at line 187 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp.

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

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