#include <DeltaNotchOdeSystem.hpp>

Inheritance diagram for DeltaNotchOdeSystem:

Collaboration diagram for DeltaNotchOdeSystem:

Public Member Functions
	DeltaNotchOdeSystem (std::vector< double > stateVariables=std::vector< double >())

	~DeltaNotchOdeSystem ()

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

Public Member Functions inherited from AbstractOdeSystem
	AbstractOdeSystem (unsigned numberOfStateVariables)

virtual	~AbstractOdeSystem ()

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

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

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)

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 Delta-Notch ODE system described by Collier et al, "Pattern formation by lateral inhibition with feedback: a mathematical model of delta-notch intercellular signalling" (Journal of Theoretical Biology 183:429-446, 1996).

Definition at line 53 of file DeltaNotchOdeSystem.hpp.

Constructor & Destructor Documentation

DeltaNotchOdeSystem::DeltaNotchOdeSystem ( std::vector< double > stateVariables = std::vector<double>() )

Todo:: extract model parameters as member variables

Default constructor.

Parameters

stateVariables optional initial conditions for state variables (only used in archiving)

The state variables are as follows:

0 - Notch concentration for this cell 1 - Delta concentration for this cell

We store the last state variable so that it can be written to file at each time step alongside the others, and visualized.

Definition at line 39 of file DeltaNotchOdeSystem.cpp.

References AbstractParameterisedSystem< std::vector< double > >::mParameters, AbstractUntemplatedParameterisedSystem::mpSystemInfo, AbstractParameterisedSystem< std::vector< double > >::SetDefaultInitialCondition(), and AbstractParameterisedSystem< std::vector< double > >::SetStateVariables().

DeltaNotchOdeSystem::~DeltaNotchOdeSystem ( )

Destructor.

Definition at line 65 of file DeltaNotchOdeSystem.cpp.

Member Function Documentation

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

virtual

Compute the RHS of the Collier et al. 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 Collier et al. system of equations).

Implements AbstractOdeSystem.

Definition at line 69 of file DeltaNotchOdeSystem.cpp.

References AbstractParameterisedSystem< std::vector< double > >::mParameters.

template<class Archive >

void DeltaNotchOdeSystem::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 65 of file DeltaNotchOdeSystem.hpp.

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

cell_based/src/odes/DeltaNotchOdeSystem.hpp
cell_based/src/odes/DeltaNotchOdeSystem.cpp

Public Member Functions

Private Member Functions

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation