IngeWntSwatCellCycleOdeSystem Class Reference

#include <IngeWntSwatCellCycleOdeSystem.hpp>

Inheritance diagram for IngeWntSwatCellCycleOdeSystem:

Collaboration diagram for IngeWntSwatCellCycleOdeSystem:

List of all members.

Public Member Functions

IngeWntSwatCellCycleOdeSystem (unsigned hypothesis, double wntLevel=0.0, const CellMutationState &rMutationState=HEALTHY)

~IngeWntSwatCellCycleOdeSystem ()

void Init ()

void SetMutationState (const CellMutationState &rMutationState)

CellMutationState & rGetMutationState ()

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)

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

CellMutationState mMutationState

unsigned mHypothesis

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 69 of file IngeWntSwatCellCycleOdeSystem.hpp.

Constructor & Destructor Documentation

IngeWntSwatCellCycleOdeSystem::IngeWntSwatCellCycleOdeSystem	(	unsigned	hypothesis,
		double	wntLevel = `0.0`,
		const CellMutationState &	rMutationState = `HEALTHY`
	)

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.
	rMutationState	affects the ODE system and is given by CryptCellMutationStates.hpp

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 31 of file IngeWntSwatCellCycleOdeSystem.cpp.

References Init(), mDa, mDc, mDca, mDct, mDd, mDdx, mDt, mDu, mDx, mDy, mKc, mKd, mKt, mMutationState, mPc, AbstractOdeSystem::mpSystemInfo, mPu, mSa, mSc, mSca, mSct, mSd, mSt, mSx, mSy, mXiC, mXiD, mXiDx, mXiX, and AbstractOdeSystem::SetInitialConditionsComponent().

IngeWntSwatCellCycleOdeSystem::~IngeWntSwatCellCycleOdeSystem ( )

Destructor.

Definition at line 154 of file IngeWntSwatCellCycleOdeSystem.cpp.

Member Function Documentation

void IngeWntSwatCellCycleOdeSystem::Init ( )

Initialise parameter values.

Definition at line 159 of file IngeWntSwatCellCycleOdeSystem.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 IngeWntSwatCellCycleOdeSystem().

void IngeWntSwatCellCycleOdeSystem::SetMutationState ( const CellMutationState & rMutationState )

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:

rMutationState

the mutation state.

Definition at line 149 of file IngeWntSwatCellCycleOdeSystem.cpp.

References mMutationState.

CellMutationState & IngeWntSwatCellCycleOdeSystem::rGetMutationState ( )

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

Returns:: mMutationState the mutation state of the cell defined by CryptCellMutationStates.hpp

Definition at line 377 of file IngeWntSwatCellCycleOdeSystem.cpp.

References mMutationState.

void IngeWntSwatCellCycleOdeSystem::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 250 of file IngeWntSwatCellCycleOdeSystem.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, mMutationState, 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 CalculateStoppingEvent().

bool IngeWntSwatCellCycleOdeSystem::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 382 of file IngeWntSwatCellCycleOdeSystem.cpp.

References EvaluateYDerivatives().

double IngeWntSwatCellCycleOdeSystem::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 391 of file IngeWntSwatCellCycleOdeSystem.cpp.

Member Data Documentation

double IngeWntSwatCellCycleOdeSystem::mk2d [private]

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

Definition at line 78 of file IngeWntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double IngeWntSwatCellCycleOdeSystem::mk3d [private]

Dimensional parameter k_3.

Definition at line 80 of file IngeWntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double IngeWntSwatCellCycleOdeSystem::mk34d [private]

Dimensional parameter k_34.

Definition at line 82 of file IngeWntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double IngeWntSwatCellCycleOdeSystem::mk43d [private]

Dimensional parameter k_2.

Definition at line 84 of file IngeWntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double IngeWntSwatCellCycleOdeSystem::mk23d [private]

Dimensional parameter k_23.

Definition at line 86 of file IngeWntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double IngeWntSwatCellCycleOdeSystem::mad [private]

Dimensional parameter a.

Definition at line 88 of file IngeWntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double IngeWntSwatCellCycleOdeSystem::mJ11d [private]

Dimensional parameter J_11.

Definition at line 90 of file IngeWntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double IngeWntSwatCellCycleOdeSystem::mJ12d [private]

Dimensional parameter J_12.

Definition at line 92 of file IngeWntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double IngeWntSwatCellCycleOdeSystem::mJ13d [private]

Dimensional parameter J_13.

Definition at line 94 of file IngeWntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double IngeWntSwatCellCycleOdeSystem::mJ61d [private]

Dimensional parameter J_13.

Definition at line 96 of file IngeWntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double IngeWntSwatCellCycleOdeSystem::mJ62d [private]

Dimensional parameter J_62.

Definition at line 98 of file IngeWntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double IngeWntSwatCellCycleOdeSystem::mJ63d [private]

Dimensional parameter J_63.

Definition at line 100 of file IngeWntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double IngeWntSwatCellCycleOdeSystem::mKm1d [private]

Dimensional parameter K_m1.

Definition at line 102 of file IngeWntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double IngeWntSwatCellCycleOdeSystem::mkpd [private]

Dimensional parameter k_p.

Definition at line 104 of file IngeWntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double IngeWntSwatCellCycleOdeSystem::mphi_r [private]

Dimensionless parameter phi_r.

Definition at line 106 of file IngeWntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double IngeWntSwatCellCycleOdeSystem::mphi_i [private]

Dimensionless parameter phi_i.

Definition at line 108 of file IngeWntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double IngeWntSwatCellCycleOdeSystem::mphi_j [private]

Dimensionless parameter phi_j.

Definition at line 110 of file IngeWntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double IngeWntSwatCellCycleOdeSystem::mphi_p [private]

Dimensionless parameter phi_p.

Definition at line 112 of file IngeWntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double IngeWntSwatCellCycleOdeSystem::mk16d [private]

Dimensional parameter k_16.

Definition at line 114 of file IngeWntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double IngeWntSwatCellCycleOdeSystem::mk61d [private]

Dimensional parameter k_61.

Definition at line 116 of file IngeWntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double IngeWntSwatCellCycleOdeSystem::mPhiE2F1 [private]

Dimensionless parameter phi_E2F1.

Definition at line 118 of file IngeWntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double IngeWntSwatCellCycleOdeSystem::mSa [private]

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

Definition at line 125 of file IngeWntSwatCellCycleOdeSystem.hpp.

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

double IngeWntSwatCellCycleOdeSystem::mSca [private]

Dimensionless parameter s_CA.

Definition at line 127 of file IngeWntSwatCellCycleOdeSystem.hpp.

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

double IngeWntSwatCellCycleOdeSystem::mSc [private]

Dimensionless parameter s_C.

Definition at line 129 of file IngeWntSwatCellCycleOdeSystem.hpp.

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

double IngeWntSwatCellCycleOdeSystem::mSct [private]

Dimensionless parameter s_CT.

Definition at line 131 of file IngeWntSwatCellCycleOdeSystem.hpp.

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

double IngeWntSwatCellCycleOdeSystem::mSd [private]

Dimensionless parameter s_D.

Definition at line 133 of file IngeWntSwatCellCycleOdeSystem.hpp.

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

double IngeWntSwatCellCycleOdeSystem::mSt [private]

Dimensionless parameter s_T.

Definition at line 135 of file IngeWntSwatCellCycleOdeSystem.hpp.

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

double IngeWntSwatCellCycleOdeSystem::mSx [private]

Dimensionless parameter s_X.

Definition at line 137 of file IngeWntSwatCellCycleOdeSystem.hpp.

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

double IngeWntSwatCellCycleOdeSystem::mSy [private]

Dimensionless parameter s_Y.

Definition at line 139 of file IngeWntSwatCellCycleOdeSystem.hpp.

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

double IngeWntSwatCellCycleOdeSystem::mDa [private]

Dimensionless parameter d_A.

Definition at line 141 of file IngeWntSwatCellCycleOdeSystem.hpp.

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

double IngeWntSwatCellCycleOdeSystem::mDca [private]

Dimensionless parameter d_CA.

Definition at line 143 of file IngeWntSwatCellCycleOdeSystem.hpp.

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

double IngeWntSwatCellCycleOdeSystem::mDc [private]

Dimensionless parameter d_C.

Definition at line 145 of file IngeWntSwatCellCycleOdeSystem.hpp.

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

double IngeWntSwatCellCycleOdeSystem::mDct [private]

Dimensionless parameter d_CT.

Definition at line 147 of file IngeWntSwatCellCycleOdeSystem.hpp.

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

double IngeWntSwatCellCycleOdeSystem::mDd [private]

Dimensionless parameter d_D.

Definition at line 149 of file IngeWntSwatCellCycleOdeSystem.hpp.

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

double IngeWntSwatCellCycleOdeSystem::mDdx [private]

Dimensionless parameter d_Dx.

Definition at line 151 of file IngeWntSwatCellCycleOdeSystem.hpp.

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

double IngeWntSwatCellCycleOdeSystem::mDt [private]

Dimensionless parameter d_T.

Definition at line 153 of file IngeWntSwatCellCycleOdeSystem.hpp.

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

double IngeWntSwatCellCycleOdeSystem::mDu [private]

Dimensionless parameter d_U.

Definition at line 155 of file IngeWntSwatCellCycleOdeSystem.hpp.

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

double IngeWntSwatCellCycleOdeSystem::mDx [private]

Dimensionless parameter d_X.

Definition at line 157 of file IngeWntSwatCellCycleOdeSystem.hpp.

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

double IngeWntSwatCellCycleOdeSystem::mDy [private]

Dimensionless parameter d_Y.

Definition at line 159 of file IngeWntSwatCellCycleOdeSystem.hpp.

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

double IngeWntSwatCellCycleOdeSystem::mKc [private]

Dimensionless parameter K_c.

Definition at line 161 of file IngeWntSwatCellCycleOdeSystem.hpp.

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

double IngeWntSwatCellCycleOdeSystem::mKd [private]

Dimensionless parameter K_D.

Definition at line 163 of file IngeWntSwatCellCycleOdeSystem.hpp.

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

double IngeWntSwatCellCycleOdeSystem::mKt [private]

Dimensionless parameter K_T.

Definition at line 165 of file IngeWntSwatCellCycleOdeSystem.hpp.

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

double IngeWntSwatCellCycleOdeSystem::mPc [private]

Dimensionless parameter p_c.

Definition at line 167 of file IngeWntSwatCellCycleOdeSystem.hpp.

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

double IngeWntSwatCellCycleOdeSystem::mPu [private]

Dimensionless parameter p_u.

Definition at line 169 of file IngeWntSwatCellCycleOdeSystem.hpp.

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

double IngeWntSwatCellCycleOdeSystem::mXiD [private]

Dimensionless parameter xi_D.

Definition at line 171 of file IngeWntSwatCellCycleOdeSystem.hpp.

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

double IngeWntSwatCellCycleOdeSystem::mXiDx [private]

Dimensionless parameter xi_Dx.

Definition at line 173 of file IngeWntSwatCellCycleOdeSystem.hpp.

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

double IngeWntSwatCellCycleOdeSystem::mXiX [private]

Dimensionless parameter xi_X.

Definition at line 175 of file IngeWntSwatCellCycleOdeSystem.hpp.

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

double IngeWntSwatCellCycleOdeSystem::mXiC [private]

Dimensionless parameter xi_C.

Definition at line 177 of file IngeWntSwatCellCycleOdeSystem.hpp.

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

CellMutationState IngeWntSwatCellCycleOdeSystem::mMutationState [private]

The mutation state of the cell

Definition at line 182 of file IngeWntSwatCellCycleOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), IngeWntSwatCellCycleOdeSystem(), rGetMutationState(), and SetMutationState().

unsigned IngeWntSwatCellCycleOdeSystem::mHypothesis [private]

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

Definition at line 189 of file IngeWntSwatCellCycleOdeSystem.hpp.

Referenced by Init().

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

/tmp/release_1.1/cancer/src/odes/IngeWntSwatCellCycleOdeSystem.hpp
/tmp/release_1.1/cancer/src/odes/IngeWntSwatCellCycleOdeSystem.cpp


Public Member Functions
	IngeWntSwatCellCycleOdeSystem (unsigned hypothesis, double wntLevel=0.0, const CellMutationState &rMutationState=HEALTHY)
	~IngeWntSwatCellCycleOdeSystem ()
void	Init ()
void	SetMutationState (const CellMutationState &rMutationState)
CellMutationState &	rGetMutationState ()
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)
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
CellMutationState	mMutationState
unsigned	mHypothesis