Stochastic simulations

Stochastic simulation algorithms. More...

Functions
C_DECL_SPEC bool rrcCallConv	getSeed (RRHandle handle, long *seed)
	Determine the current seed used by the random generator. More...
C_DECL_SPEC bool rrcCallConv	setSeed (RRHandle handle, long seed)
	Set the current seed used by the random generator. More...
C_DECL_SPEC RRCDataPtr rrcCallConv	gillespie (RRHandle handle)
	Carry out a time-course simulation using the Gillespie algorithm with variable step size. setTimeStart, setTimeEnd, etc are used to set the simulation characteristics. More...
C_DECL_SPEC RRCDataPtr rrcCallConv	gillespieEx (RRHandle handle, double timeStart, double timeEnd)
	Carry out a time-course simulation using the Gillespie algorithm based on the given arguments, time start, time end and number of points. More...
C_DECL_SPEC RRCDataPtr rrcCallConv	gillespieOnGrid (RRHandle handle)
	Carry out a time-course simulation using the Gillespie algorithm with fixed step size. setTimeStart, setTimeEnd, setNumPoints, etc are used to set the simulation characteristics. More...
C_DECL_SPEC RRCDataPtr rrcCallConv	gillespieOnGridEx (RRHandle handle, double timeStart, double timeEnd, int numberOfPoints)
	Carry out a time-course simulation using the Gillespie algorithm with fixed step size based on the given arguments, time start, time end, and number of points. More...
C_DECL_SPEC RRCDataPtr rrcCallConv	gillespieMeanOnGrid (RRHandle handle, int numberOfSimulations)
	Carry out a series of time-course simulations using the Gillespie algorithm with fixed step size, then return the average of the simulations. setTimeStart, setTimeEnd, setNumPoints, etc are used to set the simulation characteristics. More...
C_DECL_SPEC RRCDataPtr rrcCallConv	gillespieMeanOnGridEx (RRHandle handle, double timeStart, double timeEnd, int numberOfPoints, int numberOfSimulations)
	Carry out a series of time-course simulations using the Gillespie algorithm with fixed step size, then return the average of the simulations. Based on the given arguments, time start, time end, and number of points. More...
C_DECL_SPEC RRCDataPtr rrcCallConv	gillespieMeanSDOnGrid (RRHandle handle, int numberOfSimulations)
	Carry out a series of time-course simulations using the Gillespie algorithm with fixed step size, then return the average and standard deviation of the simulations. setTimeStart, setTimeEnd, setNumPoints, etc are used to set the simulation characteristics. More...
C_DECL_SPEC RRCDataPtr rrcCallConv	gillespieMeanSDOnGridEx (RRHandle handle, double timeStart, double timeEnd, int numberOfSteps, int numberOfSimulations)
	Carry out a series of time-course simulations using the Gillespie algorithm with fixed step size, then return the average and standard deviation of the simulations. Based on the given arguments, time start, time end, number of points, and number of simulations. More...

Detailed Description

Stochastic simulation algorithms.

Function Documentation

getSeed()

C_DECL_SPEC bool rrcCallConv getSeed	(	RRHandle	handle,
		long *	seed
	)

Determine the current seed used by the random generator.

Parameters

[in]	handle	Handle to a RoadRunner instance
[out]	seed	This is the value of the current seed, returned to the caller

Returns

Returns true if successful

gillespie()

C_DECL_SPEC RRCDataPtr rrcCallConv gillespie

(

RRHandle

handle

)

Carry out a time-course simulation using the Gillespie algorithm with variable step size. setTimeStart, setTimeEnd, etc are used to set the simulation characteristics.

Parameters

[in]

handle

Handle to a RoadRunner instance

Returns

Returns an array (RRCDataPtr) of columns containing the results of the simulation including string labels for the individual columns. The client is responsible for freeing the resulting RRCDataPtr structure.

gillespieEx()

C_DECL_SPEC RRCDataPtr rrcCallConv gillespieEx	(	RRHandle	handle,
		double	timeStart,
		double	timeEnd
	)

Carry out a time-course simulation using the Gillespie algorithm based on the given arguments, time start, time end and number of points.

Example:

RRCDataPtr m;
 
double timeStart = 0.0;
double timeEnd = 25;
 
m = gillespieEx (rrHandle, timeStart, timeEnd);

Parameters

[in]	handle	Handle to a RoadRunner instance
[in]	timeStart	Time start
[in]	timeEnd	Time end

Returns

Returns an array (RRCDataPtr) of columns containing the results of the simulation including string labels for the individual columns. The client is responsible for freeing the resulting RRCDataPtr structure.

gillespieMeanOnGrid()

C_DECL_SPEC RRCDataPtr rrcCallConv gillespieMeanOnGrid	(	RRHandle	handle,
		int	numberOfSimulations
	)

Carry out a series of time-course simulations using the Gillespie algorithm with fixed step size, then return the average of the simulations. setTimeStart, setTimeEnd, setNumPoints, etc are used to set the simulation characteristics.

Parameters

[in]	handle	Handle to a RoadRunner instance
[in]	numberOfSimulations	Number of simulations to perform

Returns

Returns an array (RRCDataPtr) of columns containing the average of the results of the simulations including string labels for the individual columns. The client is responsible for freeing the resulting RRCDataPtr structure.

gillespieMeanOnGridEx()

C_DECL_SPEC RRCDataPtr rrcCallConv gillespieMeanOnGridEx	(	RRHandle	handle,
		double	timeStart,
		double	timeEnd,
		int	numberOfPoints,
		int	numberOfSimulations
	)

Carry out a series of time-course simulations using the Gillespie algorithm with fixed step size, then return the average of the simulations. Based on the given arguments, time start, time end, and number of points.

Example:

RRCDataPtr m;
 
double timeStart = 0.0;
double timeEnd = 25;
int numberOfPoints = 200;
int numberOfSimulations = 10;
 
m = gillespieMeanOnGridEx (rrHandle, timeStart, timeEnd, numberOfPoints, numberOfSimulations);

Parameters

[in]	handle	Handle to a RoadRunner instance
[in]	timeStart	Time start
[in]	timeEnd	Time end
[in]	numberOfPoints	Fixed number of points to generate
[in]	numberOfSimulations	Number of simulations to perform

Returns

Returns an array (RRCDataPtr) of columns containing the average of the results of the simulation including string labels for the individual columns. The client is responsible for freeing the resulting RRCDataPtr structure.

gillespieMeanSDOnGrid()

C_DECL_SPEC RRCDataPtr rrcCallConv gillespieMeanSDOnGrid	(	RRHandle	handle,
		int	numberOfSimulations
	)

Carry out a series of time-course simulations using the Gillespie algorithm with fixed step size, then return the average and standard deviation of the simulations. setTimeStart, setTimeEnd, setNumPoints, etc are used to set the simulation characteristics.

Parameters

[in]	handle	Handle to a RoadRunner instance
[in]	numberOfSimulations	Number of simulations to perform

Returns

Returns an array (RRCDataPtr) of columns containing the average of the results of the simulations including string labels for the individual columns. The averages are in Data and the standard deviations are in Weights. The client is responsible for freeing the resulting RRCDataPtr structure.

gillespieMeanSDOnGridEx()

C_DECL_SPEC RRCDataPtr rrcCallConv gillespieMeanSDOnGridEx	(	RRHandle	handle,
		double	timeStart,
		double	timeEnd,
		int	numberOfSteps,
		int	numberOfSimulations
	)

Carry out a series of time-course simulations using the Gillespie algorithm with fixed step size, then return the average and standard deviation of the simulations. Based on the given arguments, time start, time end, number of points, and number of simulations.

Example:

RRCDataPtr m;
 
double timeStart = 0.0;
double timeEnd = 25;
int numberOfPoints = 200;
int numberOfSimulations = 10;
 
m = gillespieMeanSDOnGridEx (rrHandle, timeStart, timeEnd, numberOfPoints, numberOfSimulations);

Parameters

[in]	handle	Handle to a RoadRunner instance
[in]	timeStart	Time start
[in]	timeEnd	Time end
[in]	numberOfPoints	Fixed number of points to generate
[in]	numberOfSimulations	Number of simulations to perform

Returns

Returns an array (RRCDataPtr) of columns containing the average of the results of the simulation including string labels for the individual columns. The average values are in Data and the standard deviations are in Weights. The client is responsible for freeing the resulting RRCDataPtr structure.

gillespieOnGrid()

C_DECL_SPEC RRCDataPtr rrcCallConv gillespieOnGrid

(

RRHandle

handle

)

Carry out a time-course simulation using the Gillespie algorithm with fixed step size. setTimeStart, setTimeEnd, setNumPoints, etc are used to set the simulation characteristics.

Parameters

[in]

handle

Handle to a RoadRunner instance

Returns

Returns an array (RRCDataPtr) of columns containing the results of the simulation including string labels for the individual columns. The client is responsible for freeing the resulting RRCDataPtr structure.

gillespieOnGridEx()

C_DECL_SPEC RRCDataPtr rrcCallConv gillespieOnGridEx	(	RRHandle	handle,
		double	timeStart,
		double	timeEnd,
		int	numberOfPoints
	)

Carry out a time-course simulation using the Gillespie algorithm with fixed step size based on the given arguments, time start, time end, and number of points.

Example:

RRCDataPtr m;
 
double timeStart = 0.0;
double timeEnd = 25;
int numberOfPoints = 200;
 
m = gillespieOnGridEx (rrHandle, timeStart, timeEnd, numberOfPoints);

Parameters

[in]	handle	Handle to a RoadRunner instance
[in]	timeStart	Time start
[in]	timeEnd	Time end
[in]	numberOfPoints	Fixed number of points to generate

Returns

Returns an array (RRCDataPtr) of columns containing the results of the simulation including string labels for the individual columns. The client is responsible for freeing the resulting RRCDataPtr structure.

setSeed()

C_DECL_SPEC bool rrcCallConv setSeed	(	RRHandle	handle,
		long	seed
	)

Set the current seed used by the random generator.

Parameters

[in]	handle	Handle to a RoadRunner instance
[out]	seed	This is the value the caller will set the seed to

Returns

Returns true if successful