WntCellCycleOdeSystem Class Reference

#include <WntCellCycleOdeSystem.hpp>

Collaboration diagram for WntCellCycleOdeSystem:

Public Member Functions
	WntCellCycleOdeSystem (double wntLevel=0.0, boost::shared_ptr< AbstractCellMutationState > pMutationState=boost::shared_ptr< AbstractCellMutationState >(), std::vector< double > stateVariables=std::vector< double >())
	~WntCellCycleOdeSystem ()
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
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	ma2d
double	ma3d
double	ma4d
double	ma5d
double	mk16d
double	mk61d
double	mPhiE2F1
boost::shared_ptr < AbstractCellMutationState >	mpMutationState
double	mWntLevel
Friends
class	boost::serialization::access

Detailed Description

Represents the Mirams et al. system of ODEs, based on Swat et al. (2004) [doi:10.1093/bioinformatics/bth110] and a simple Wnt model (unpublished)

The variables are

0. r = pRb 1. e = E2F1 2. i = CycD (inactive) 3. j = CycD (active) 4. p = pRb-p 5. c = destruction complex (Active) 6. b1 = Beta-Catenin (from 1st allele) 7. b2 = Beta-Catenin (from 1st allele) 8. WntLevel

Definition at line 64 of file WntCellCycleOdeSystem.hpp.

Constructor & Destructor Documentation

WntCellCycleOdeSystem::WntCellCycleOdeSystem	(	double	wntLevel = `0.0`,
		boost::shared_ptr< AbstractCellMutationState >	pMutationState = `boost::shared_ptr<AbstractCellMutationState>()`,
		std::vector< double >	stateVariables = `std::vector<double>()`
	)

Constructor.

Parameters:

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

State variables.

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. c = APC (Active) 6. b1 = Beta-Catenin (1st allele's copy) 7. b2 = Beta-Catenin (2nd allele's copy) 8. wntLevel

Definition at line 32 of file WntCellCycleOdeSystem.cpp.

References Init(), ma2d, ma3d, ma4d, ma5d, mpMutationState, AbstractUntemplatedParameterisedSystem::mpSystemInfo, AbstractParameterisedSystem< std::vector< double > >::SetDefaultInitialCondition(), and AbstractParameterisedSystem< std::vector< double > >::SetStateVariables().

WntCellCycleOdeSystem::~WntCellCycleOdeSystem ( )

Destructor.

Definition at line 109 of file WntCellCycleOdeSystem.cpp.

Member Function Documentation

double WntCellCycleOdeSystem::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:: function value - giving CVODE an estimate of how close we are to the root.

Reimplemented from AbstractOdeSystem.

Definition at line 292 of file WntCellCycleOdeSystem.cpp.

bool WntCellCycleOdeSystem::CalculateStoppingEvent	(	double	time,
		const std::vector< double > &	rY
	)			`[virtual]`

This also contains a calculation of dY[1], copied from EvaluateYDerivatives. Ensure they do not get out of sync!

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 we have reached the stopping event

Reimplemented from AbstractOdeSystem.

Definition at line 278 of file WntCellCycleOdeSystem.cpp.

References mad, mJ12d, mJ62d, mk2d, mkpd, and mPhiE2F1.

void WntCellCycleOdeSystem::EvaluateYDerivatives	(	double	time,
		const std::vector< double > &	rY,
		std::vector< double > &	rDY
	)			`[virtual]`

Compute the RHS of the WntCellCycle 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 181 of file WntCellCycleOdeSystem.cpp.

References ma2d, ma3d, ma4d, ma5d, mad, mJ11d, mJ12d, mJ13d, mJ61d, mJ62d, mJ63d, mk16d, mk23d, mk2d, mk34d, mk3d, mk43d, mk61d, mKm1d, mkpd, mphi_i, mphi_j, mphi_p, mphi_r, mPhiE2F1, and mpMutationState.