bdm::GeneRegulation Class Reference

#include <gene_regulation.h>

Inheritance diagram for bdm::GeneRegulation:

Collaboration diagram for bdm::GeneRegulation:

Public Member Functions
	GeneRegulation ()
virtual	~GeneRegulation ()=default
void	Initialize (const NewAgentEvent &event) override
void	AddGene (const std::function< real_t(real_t, real_t)> &first_derivative, real_t initial_concentration)
const std::vector< real_t > &	GetValues () const
void	Run (Agent *agent) override
Public Member Functions inherited from bdm::Behavior
	Behavior ()
virtual	~Behavior ()=default
virtual Behavior *	New () const =0
	Create a new instance of this object using the default constructor. More...
virtual Behavior *	NewCopy () const =0
	Create a new copy of this behavior. More...
virtual void	Update (const NewAgentEvent &event)
void	AlwaysCopyToNew ()
	Always copy this behavior to new agents. More...
void	NeverCopyToNew ()
	Never copy this behavior to new agents. More...
void	CopyToNewIf (const std::initializer_list< NewAgentEventUid > &uids)
void	AlwaysRemoveFromExisting ()
void	NeverRemoveFromExisting ()
void	RemoveFromExistingIf (const std::initializer_list< NewAgentEventUid > &uids)
bool	WillBeCopied (NewAgentEventUid event) const
bool	WillBeRemoved (NewAgentEventUid event) const
void *	operator new (size_t size)
void	operator delete (void *p)

Private Member Functions
	BDM_BEHAVIOR_HEADER (GeneRegulation, Behavior, 1)

Private Attributes
std::vector< real_t >	concentrations_ = {}
	Store the current concentration for each gene. More...
std::vector< std::function< real_t(real_t, real_t)> >	first_derivatives_ = {}

Detailed Description

This behavior simulates expression of genes and contains all required additional variables for tracking of the concentration of proteins. Thus, it can work with any type of agent. It has the implementation of Euler and Runge-Kutta numerical methods for solving ODE. Both methods implemented inside the body of method Run(). The user determines which method is picked in particular simulation through variable Param::numerical_ode_solver.

Definition at line 36 of file gene_regulation.h.

Constructor & Destructor Documentation

GeneRegulation()

bdm::GeneRegulation::GeneRegulation ( )

inline

Definition at line 40 of file gene_regulation.h.

~GeneRegulation()

virtual bdm::GeneRegulation::~GeneRegulation ( )

virtualdefault

Member Function Documentation

AddGene()

void bdm::GeneRegulation::AddGene ( const std::function< real_t(real_t, real_t)> &  first_derivative, real_t  initial_concentration  )

inline

AddGene adds a new differential equation.

Parameters

first_derivative	differential equation in the form: slope = f(time, last_concentration) – e.g.: [](real_t time, real_t last_concentration) { return 1 - time * last_concentration; }
initial_concentration

Definition at line 66 of file gene_regulation.h.

BDM_BEHAVIOR_HEADER()

bdm::GeneRegulation::BDM_BEHAVIOR_HEADER ( GeneRegulation  , Behavior  , 1    )

private

GetValues()

const std::vector<real_t>& bdm::GeneRegulation::GetValues ( ) const

inline

Definition at line 72 of file gene_regulation.h.

Initialize()

void bdm::GeneRegulation::Initialize ( const NewAgentEvent &  event )

inlineoverridevirtual

This method is called to initialize new behaviors that are created during a NewAgentEvent. Override this method to initialize attributes of your own Behavior subclasses. NB: Don't forget to call the implementation of the base class first. Base::Initialize(event); Failing to do so will result in errors.

Reimplemented from bdm::Behavior.

Definition at line 44 of file gene_regulation.h.

Run()

void bdm::GeneRegulation::Run ( Agent *  agent )

inlineoverridevirtual

Method Run() contains the implementation for Runge-Khutta and Euler methods for solving ODE.

Implements bdm::Behavior.

Definition at line 76 of file gene_regulation.h.

Member Data Documentation

concentrations_

std::vector<real_t> bdm::GeneRegulation::concentrations_ = {}

private

Store the current concentration for each gene.

Definition at line 112 of file gene_regulation.h.

first_derivatives_

std::vector<std::function<real_t(real_t, real_t)> > bdm::GeneRegulation::first_derivatives_ = {}

private

Store the gene differential equations, which define how the concentration change. New functions can be added through method AddGene()

Definition at line 117 of file gene_regulation.h.

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

• core/behavior/gene_regulation.h