Computational Systems Biology
Sauro Lab
University of Washington
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1. SBW
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6. Optimization
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maintained by Frank Bergmann
 
 
 
 

RoadRunner API

Provides Simulator API

Service: sim

High Performance ODE Simulator using CVODE and NLEQ2

string getName()

Returns the name of module

string getVersion()

Returns the version number of the module

string getAuthor()

Returns the name of the module author

string getDescription()

Returns a description of the module

string getDisplayName()

Returns the display name of the module

string getCopyright()

Returns the copyright string for the module

string getURL()

Returns the URL string associated with the module (if any)

string getCSharpCode()

Returns the current generated source code

void loadSBML(string)

Load SBML into simulator

string getSBML()

Returns the currently loaded model as SBML

void setTimeStart(double)

Set the time start for the simulation

void setTimeEnd(double)

Set the time end for the simulation

void setNumPoints(int)

Set the number of points to generate during the simulation

void reset()

reset the simulator back to the initial conditions specified in the SBML model

void changeInitialConditions(double[])

Change the initial conditions to another concentration vector

double[][] simulate()

Carry out a time course simulation

double[][] simulateEx(double,double,int)

Extension method to simulate (time start, time end, number of points). This routine resets the model to its initial condition before running the simulation (unlike simulate())

double[] getReactionRates()

Returns the current vector of reactions rates

double[] getRatesOfChange()

Returns the current vector of rates of change

{} getSpeciesNames()

Returns a list of floating species names: This method is deprecated, please use getFloatingSpeciesNames()

{} getReactionNames()

Returns a list of reaction names

string getCapabilities()

Get Simulator Capabilities

void setCapabilities(string)

Set Simulator Capabilites

int getNumberOfCompartments()

Get the number of compartments

void setCompartmentByIndex(int,double)

Sets the value of a compartment by its index

double getCompartmentByIndex(int)

Returns the value of a compartment by its index

void setCompartmentVolumes(double[])

Returns the value of a compartment by its index

{} getCompartmentNames()

Gets the list of compartment names

int getNumberOfBoundarySpecies()

Get the number of boundary species

void setBoundarySpeciesByIndex(int,double)

Sets the value of a boundary species by its index

double getBoundarySpeciesByIndex(int)

Returns the value of a boundary species by its index

double[] getBoundarySpeciesConcentrations()

Returns an array of boundary species concentrations

void setBoundarySpeciesConcentrations(double[])

Set the concentrations for all boundary species in the model

{} getBoundarySpeciesNames()

Gets the list of boundary species names

int getNumberOfFloatingSpecies()

Get the number of floating species

void setFloatingSpeciesByIndex(int,double)

Sets the value of a floating species by its index

double getFloatingSpeciesByIndex(int)

Returns the value of a floating species by its index

double[] getFloatingSpeciesConcentrations()

Returns an array of floating species concentrations

void setFloatingSpeciesConcentrations(double[])

Set the concentrations for all floating species in the model

{} getFloatingSpeciesNames()

Returns a list of floating species names

int getNumberOfGlobalParameters()

Get the number of global parameters

void setGlobalParameterByIndex(int,double)

Sets the value of a global parameter by its index

double getGlobalParameterByIndex(int)

Returns the value of a global parameter by its index

void setGlobalParameterValues(double[])

Set the values for all global parameters in the model

double[] getGlobalParameterValues()

Get the values for all global parameters in the model

{} getGlobalParameterNames()

Gets the list of parameter names

void setValue(string,double)

Sets the value of the given species or global parameter to the given value (not of local parameters)

double getValue(string)

Gets the Value of the given species or global parameter (not of local parameters)

{} getAllGlobalParameterTupleList()

Returns a list of global parameter tuples: { {parameter Name, value},…

int getNumberOfLocalParameters(int)

Get the number of local parameters for a given reaction

void setLocalParameterByIndex(int,int,double)

Sets the value of a global parameter by its index

double getLocalParameterByIndex(int,int)

Returns the value of a global parameter by its index

void setLocalParameterValues(int,double[])

Set the values for all global parameters in the model

double[] getLocalParameterValues(int)

Get the values for all global parameters in the model

{} getLocalParameterNames(int)

Gets the list of parameter names

{} getAllLocalParameterTupleList()

Returns a list of global parameter tuples: { {parameter Name, value},…

int getNumberOfReactions()

Get the number of reactions

double getReactionRate(int)

Returns the rate of a reaction by its index

double getRateOfChange(int)

Returns the rate of changes of a species by its index

{} getRateOfChangeNames()

Returns the names given to the rate of change of the floating species

void setSelectionList({})

Set the columns to be returned by simulate() or simulateEx(), valid symbol names include time, species names, , volume, reaction rates and rates of change (speciesName')

double[] getRatesOfChangeEx(double[])

Returns the rates of changes given an array of new floating species concentrations

double[] getReactionRatesEx(double[])

Returns the rates of changes given an array of new floating species concentrations

double oneStep(double,double)

Carry out a single integration step using a stepsize as indicated in the method call

double steadyState()

Compute the steady state of the model, returns the sum of squares of the solution

double[][] getReducedJacobian()

Compute the reduced Jacobian at the current operating point

double[][] getFullJacobian()

Compute the full Jacobian at the current operating point

double[][] getLinkMatrix()

Returns the Link Matrix for the currently loaded model

double[][] getNrMatrix()

Returns the reduced stoichiometry matrix (Nr) for the currently loaded model

double[][] getL0Matrix()

Returns the L0 matrix for the currently loaded model

double[][] getStoichiometryMatrix()

Returns the stoichiometry matrix for the currently loaded model

double[][] getConservationMatrix()

Returns the conservation matrix (gamma) for the currently loaded model

int getNumberOfDependentSpecies()

Returns the number of dependent species in the model

int getNumberOfIndependentSpecies()

Returns the number of independent species in the model

double getUnScaledElasticity(string,string)

Returns the elasticity of a given reaction to a given parameter. Parameters can be boundary species or global parameters

double[][] getUnscaledElasticityMatrix()

Compute the unscaled species elasticity matrix at the current operating point

double[][] getScaledElasticityMatrix()

Compute the unscaled elasticity matrix at the current operating point

double getUnscaledFloatingSpeciesElasticity(string,string)

Compute the unscaled elasticity for a given reaction and given species

double getScaledFloatingSpeciesElasticity(string,string)

Compute the scaled elasticity for a given reaction and given species

double[][] getUnscaledConcentrationControlCoefficientMatrix()

Compute the matrix of unscaled concentration control coefficients

double[][] getScaledConcentrationControlCoefficientMatrix()

Compute the matrix of scaled concentration control coefficients

double[][] getUnscaledFluxControlCoefficientMatrix()

Compute the matrix of unscaled flux control coefficients

double[][] getScaledFluxControlCoefficientMatrix()

Compute the matrix of scaled flux control coefficients

double getUnscaledConcentrationControlCoefficient(string,string,string)

Compute the value for a particular unscaled concentration control coefficients with respect to a local parameter

double getScaledConcentrationControlCoefficient(string,string,string)

Compute the value for a particular scaled concentration control coefficients with respect to a local parameter

double getUnscaledConcentrationControlCoefficient(string,string)

Compute the value for a particular concentration control coefficient, permitted parameters include global parameters, boundary conditions and conservation totals

double getScaledConcentrationControlCoefficient(string,string)

Compute the value for a particular scaled concentration control coefficients with respect to a global or boundary species parameter

double getUnscaledFluxControlCoefficient(string,string,string)

Compute the value for a particular unscaled flux control coefficients with respect to a local parameter

double getUnscaledFluxControlCoefficient(string,string)

Compute the value for a particular flux control coefficient, permitted parameters include global parameters, boundary conditions and conservation totals

double getScaledFluxControlCoefficient(string,string,string)

Compute the value for a particular scaled flux control coefficients with respect to a local parameter

double getScaledFluxControlCoefficient(string,string)

Compute the value for a particular scaled flux control coefficients with respect to a global or boundary species parameter

double getuCC(string,string)

Get unscaled control coefficient with respect to a global parameter

double getCC(string,string)

Get scaled control coefficient with respect to a global parameter

double getuEE(string,string)

Get unscaled elasticity coefficient with respect to a global parameter or species

double getEE(string,string)

Get scaled elasticity coefficient with respect to a global parameter or species

double[][] getFrequencyResponse(double,int,int,string,string,boolean,boolean)

Compute the frequency response, startW, Number Of Decades, Number of Points, parameterName, variableName

void computeContinuation(double,int,string)

Derpar Continuation, stepSize = stepsize; independentVariable = index to parameter; parameterType = {'globalParameter', 'boundarySpecies'

 
sbw/roadrunner/api.txt · Last modified: 2007/01/12 07:53 (external edit)
 

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