Mirams2010WntOdeSystem Class Reference

#include <Mirams2010WntOdeSystem.hpp>

Inheritance diagram for Mirams2010WntOdeSystem:

Collaboration diagram for Mirams2010WntOdeSystem:

List of all members.

Public Member Functions

Mirams2010WntOdeSystem (double wntLevel=0.0, boost::shared_ptr< AbstractCellMutationState > pMutationState=boost::shared_ptr< AbstractCellMutationState >(), std::vector< double > stateVariables=std::vector< double >())

~Mirams2010WntOdeSystem ()

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)

double GetWntLevel () const

Private Member Functions

template<class Archive>

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

Private Attributes

double mA

double mB

double mC

double mD

double mE

double mF

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 (2004) [doi:10.1093/bioinformatics/bth110] and a simple Wnt model (unpublished)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

6. b1 = Beta-Catenin (from 1st allele) 7. b2 = Beta-Catenin (from 1st allele) 8. WntLevel

Definition at line 59 of file Mirams2010WntOdeSystem.hpp.

Constructor & Destructor Documentation

Mirams2010WntOdeSystem::Mirams2010WntOdeSystem	(	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. b1 = Beta-Catenin (1st allele's copy) 1. b2 = Beta-Catenin (2nd allele's copy) 2. wntLevel

Definition at line 31 of file Mirams2010WntOdeSystem.cpp.

References Init(), mA, mB, mC, mD, mF, mpMutationState, AbstractParameterisedSystem< std::vector< double > >::mpSystemInfo, AbstractOdeSystem::SetDefaultInitialCondition(), and AbstractOdeSystem::SetStateVariables().

Mirams2010WntOdeSystem::~Mirams2010WntOdeSystem ( )

Destructor.

Definition at line 82 of file Mirams2010WntOdeSystem.cpp.

Member Function Documentation

template<class Archive>

void Mirams2010WntOdeSystem::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 94 of file Mirams2010WntOdeSystem.hpp.

void Mirams2010WntOdeSystem::Init ( )

Initialise parameter values.

Definition at line 87 of file Mirams2010WntOdeSystem.cpp.

References mA, mB, mC, mD, mE, and mF.

Referenced by Mirams2010WntOdeSystem().

void Mirams2010WntOdeSystem::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 77 of file Mirams2010WntOdeSystem.cpp.

References mpMutationState.

const boost::shared_ptr< AbstractCellMutationState > Mirams2010WntOdeSystem::GetMutationState ( ) const

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

Returns:: mpMutationState

Definition at line 143 of file Mirams2010WntOdeSystem.cpp.

References mpMutationState.

void Mirams2010WntOdeSystem::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 98 of file Mirams2010WntOdeSystem.cpp.

References mA, mB, mC, mD, mE, mF, and mpMutationState.

double Mirams2010WntOdeSystem::GetWntLevel ( ) const

Get method for mWntLevel.

Definition at line 166 of file Mirams2010WntOdeSystem.cpp.

References mWntLevel.

Member Data Documentation

double Mirams2010WntOdeSystem::mA [private]

Parameters for the Mirams et al. (2010) model Dimensional parameter a.

Definition at line 68 of file Mirams2010WntOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), Init(), and Mirams2010WntOdeSystem().

double Mirams2010WntOdeSystem::mB [private]

Dimensional parameter b.

Definition at line 70 of file Mirams2010WntOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), Init(), and Mirams2010WntOdeSystem().

double Mirams2010WntOdeSystem::mC [private]

Dimensional parameter c.

Definition at line 72 of file Mirams2010WntOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), Init(), and Mirams2010WntOdeSystem().

double Mirams2010WntOdeSystem::mD [private]

Dimensional parameter d.

Definition at line 74 of file Mirams2010WntOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), Init(), and Mirams2010WntOdeSystem().

double Mirams2010WntOdeSystem::mE [private]

Dimensional parameter e.

Definition at line 76 of file Mirams2010WntOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double Mirams2010WntOdeSystem::mF [private]

Dimensional parameter f.

Definition at line 78 of file Mirams2010WntOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), Init(), and Mirams2010WntOdeSystem().

boost::shared_ptr<AbstractCellMutationState> Mirams2010WntOdeSystem::mpMutationState [private]

The mutation state of the cell (this affects the ODE system).

Definition at line 81 of file Mirams2010WntOdeSystem.hpp.

Referenced by EvaluateYDerivatives(), GetMutationState(), Mirams2010WntOdeSystem(), and SetMutationState().

double Mirams2010WntOdeSystem::mWntLevel [private]

The Wnt level (this affects the ODE system).

Definition at line 84 of file Mirams2010WntOdeSystem.hpp.

Referenced by GetWntLevel().

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

crypt/src/odes/Mirams2010WntOdeSystem.hpp
crypt/src/odes/Mirams2010WntOdeSystem.cpp


Public Member Functions
	Mirams2010WntOdeSystem (double wntLevel=0.0, boost::shared_ptr< AbstractCellMutationState > pMutationState=boost::shared_ptr< AbstractCellMutationState >(), std::vector< double > stateVariables=std::vector< double >())
	~Mirams2010WntOdeSystem ()
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)
double	GetWntLevel () const
Private Member Functions
template<class Archive>
void	serialize (Archive &archive, const unsigned int version)
Private Attributes
double	mA
double	mB
double	mC
double	mD
double	mE
double	mF
boost::shared_ptr < AbstractCellMutationState >	mpMutationState
double	mWntLevel
Friends
class	boost::serialization::access