Simulation

Simulations and other numerical analysis. More...

Functions
BEGIN_C_DECLS TCAPIEXPORT tc_matrix	tc_simulateDeterministic (double startTime, double endTime, int numSteps)
	simulate using LSODA numerical integrator
TCAPIEXPORT tc_matrix	tc_simulateStochastic (double startTime, double endTime, int numSteps)
	simulate using exact stochastic algorithm
TCAPIEXPORT tc_matrix	tc_simulateHybrid (double startTime, double endTime, int numSteps)
	simulate using Hybrid algorithm/deterministic algorithmparam double start time
TCAPIEXPORT tc_matrix	tc_simulateTauLeap (double startTime, double endTime, int numSteps)
	simulate using Tau Leap stochastic algorithm
TCAPIEXPORT tc_matrix	tc_getSteadyState ()
	bring the system to steady state
TCAPIEXPORT tc_matrix	tc_steadyStateScan (const char *param, double start, double end, int numSteps)
	calculate steady state for each value of a parameter
TCAPIEXPORT tc_matrix	tc_steadyStateScan2D (const char *param1, double start1, double end1, int numSteps1, const char *param2, double start2, double end2, int numSteps2)
	calculate steady state for each value of two parameters
TCAPIEXPORT tc_matrix	tc_getJacobian ()
	get the Jacobian at the current state
TCAPIEXPORT tc_matrix	tc_getEigenvalues ()
	get the eigenvalues of the Jacobian at the current state
TCAPIEXPORT tc_matrix	tc_getUnscaledElasticities ()
	unscaled elasticities
TCAPIEXPORT tc_matrix	tc_getUnscaledConcentrationCC ()
	unscaled elasticities
TCAPIEXPORT tc_matrix	tc_getUnscaledFluxCC ()
	unscaled flux control coefficients
TCAPIEXPORT tc_matrix	tc_getScaledElasticities ()
	scaled elasticities
TCAPIEXPORT tc_matrix	tc_getScaledConcentrationCC ()
	scaled concentration control coefficients
TCAPIEXPORT tc_matrix	tc_getScaledFluxCC ()
	scaled flux control coefficients
TCAPIEXPORT tc_matrix	tc_reducedStoichiometry ()
	reduced stoichiometry
TCAPIEXPORT tc_matrix	tc_elementaryFluxModes ()
	elementary flux modes
TCAPIEXPORT tc_matrix	tc_LMatrix ()
	left nullspace of the stoichiometry matrix
TCAPIEXPORT tc_matrix	tc_KMatrix ()
	right nullspace of the stoichiometry matrix
TCAPIEXPORT tc_matrix	tc_calcFluxes ()
	get current flux values
TCAPIEXPORT tc_matrix	tc_calcDerivatives ()
	get current rates of change (derivaives)
TCAPIEXPORT void	tc_updateParameters (tc_matrix params)
	update the model parameters just for simulation purposes, i.e. not the actual model itself this function will be much faster than using tc_setParameters
TCAPIEXPORT void	tc_updateParameter (const char *param, double value)
	update a model parameter just for simulation purposes, i.e. not the actual model itself this function will be much faster than using tc_setParameter
TCAPIEXPORT tc_matrix	tc_optimize (const char *formulaOrFile)
	Maximize the given formula or fit the data is the given filename, depending on whether or not the input is a filename. The optimization is done using genetic algorithms, so a distribution of optimal parameters is generated. All parameters in the model will be used where the parameter's min and max values are different (i.e. parameter is variable)
TCAPIEXPORT void	tc_enableAssignmentRulesReordering (int)
	enable or disable assignment rule reordering. reordering prevents possible errors due to the order of assignment rules. Default: enabled

---

Detailed Description

Simulations and other numerical analysis.

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Function Documentation

TCAPIEXPORT tc_matrix tc_calcDerivatives

(

)

get current rates of change (derivaives)

Returns:

tc_matrix

TCAPIEXPORT tc_matrix tc_calcFluxes

(

)

get current flux values

Returns:

tc_matrix

TCAPIEXPORT tc_matrix tc_elementaryFluxModes

(

)

elementary flux modes

Returns:

tc_matrix

TCAPIEXPORT void tc_enableAssignmentRulesReordering

(

int

)

enable or disable assignment rule reordering. reordering prevents possible errors due to the order of assignment rules. Default: enabled

Parameters:

int	0=disable, 1=enable

TCAPIEXPORT tc_matrix tc_getEigenvalues

(

)

get the eigenvalues of the Jacobian at the current state

Returns:

tc_matrix matrix with 1 row and n columns, each containing an eigenvalue

TCAPIEXPORT tc_matrix tc_getJacobian

(

)

get the Jacobian at the current state

Returns:

tc_matrix matrix with n rows and n columns, where n = number of species

TCAPIEXPORT tc_matrix tc_getScaledConcentrationCC

(

)

scaled concentration control coefficients

Returns:

tc_matrix

TCAPIEXPORT tc_matrix tc_getScaledElasticities

(

)

scaled elasticities

Returns:

tc_matrix

TCAPIEXPORT tc_matrix tc_getScaledFluxCC

(

)

scaled flux control coefficients

Returns:

tc_matrix

TCAPIEXPORT tc_matrix tc_getSteadyState

(

)

bring the system to steady state

Returns:

tc_matrix matrix with 1 row and n columns, where n = number of species

TCAPIEXPORT tc_matrix tc_getUnscaledConcentrationCC

(

)

unscaled elasticities

unscaled concentration control coefficients

Returns:

tc_matrix

TCAPIEXPORT tc_matrix tc_getUnscaledElasticities

(

)

unscaled elasticities

Returns:

tc_matrix

TCAPIEXPORT tc_matrix tc_getUnscaledFluxCC

(

)

unscaled flux control coefficients

Returns:

tc_matrix

TCAPIEXPORT tc_matrix tc_KMatrix

(

)

right nullspace of the stoichiometry matrix

Returns:

tc_matrix

TCAPIEXPORT tc_matrix tc_LMatrix

(

)

left nullspace of the stoichiometry matrix

Returns:

tc_matrix

TCAPIEXPORT tc_matrix tc_optimize

(

const char *

formulaOrFile

)

Maximize the given formula or fit the data is the given filename, depending on whether or not the input is a filename. The optimization is done using genetic algorithms, so a distribution of optimal parameters is generated. All parameters in the model will be used where the parameter's min and max values are different (i.e. parameter is variable)

Parameters:

const

char * formula to maximize or filename with data (csv or tab-delimited)

Returns:

tc_matrix a population of parameters

TCAPIEXPORT tc_matrix tc_reducedStoichiometry

(

)

reduced stoichiometry

Returns:

tc_matrix

BEGIN_C_DECLS TCAPIEXPORT tc_matrix tc_simulateDeterministic	(	double	startTime,
		double	endTime,
		int	numSteps
	)

simulate using LSODA numerical integrator

Parameters:

double	start time
double	end time
int	number of steps in the output

Returns:

tc_matrix matrix of concentration or particles

TCAPIEXPORT tc_matrix tc_simulateHybrid	(	double	startTime,
		double	endTime,
		int	numSteps
	)

simulate using Hybrid algorithm/deterministic algorithmparam double start time

Parameters:

double	end time
int	number of steps in the output

Returns:

tc_matrix matrix of concentration or particles

TCAPIEXPORT tc_matrix tc_simulateStochastic	(	double	startTime,
		double	endTime,
		int	numSteps
	)

simulate using exact stochastic algorithm

Parameters:

double	start time
double	end time
int	number of steps in the output

Returns:

tc_matrix matrix of concentration or particles

TCAPIEXPORT tc_matrix tc_simulateTauLeap	(	double	startTime,
		double	endTime,
		int	numSteps
	)

simulate using Tau Leap stochastic algorithm

Parameters:

double	start time
double	end time
int	number of steps in the output

Returns:

tc_matrix matrix of concentration or particles

TCAPIEXPORT tc_matrix tc_steadyStateScan	(	const char *	param,
		double	start,
		double	end,
		int	numSteps
	)

calculate steady state for each value of a parameter

Parameters:

char	* parameter name
double	start value
double	end value
int	number of steps in the output

Returns:

tc_matrix matrix of concentration or particles

TCAPIEXPORT tc_matrix tc_steadyStateScan2D	(	const char *	param1,
		double	start1,
		double	end1,
		int	numSteps1,
		const char *	param2,
		double	start2,
		double	end2,
		int	numSteps2
	)

calculate steady state for each value of two parameters

Parameters:

char	* first parameter name
double	start value for parameter 1
double	end value for parameter 1
int	number of steps in parameter 1
char	* second parameter name
double	start value for parameter 2
double	end value for parameter 2
int	number of steps in parameter 2

Returns:

tc_matrix matrix of concentration or particles

TCAPIEXPORT void tc_updateParameter	(	const char *	param,
		double	value
	)

update a model parameter just for simulation purposes, i.e. not the actual model itself this function will be much faster than using tc_setParameter

Parameters:

string	parameter name
double	parameter value

TCAPIEXPORT void tc_updateParameters

(

tc_matrix

params

)

update the model parameters just for simulation purposes, i.e. not the actual model itself this function will be much faster than using tc_setParameters

Parameters:

tc_matrix

parameters with row names