Computational Systems Biology
Sauro Lab
University of Washington
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Software Downloads:

1. SBW
2. JDesigner
3. Jarnac
4. WinSCAMP
5. Matlab Interface
6. Optimization
6. Bifurcation
 
maintained by Frank Bergmann
 
 
 
 

Jarnac API

Service: msim

Multi-simulation interface, most calls require the model handle as the first argument

int createModel ()

Start a new model instance, returns model handle

void freeModel (int modelHandle)

Destroy a model given it's model handle

void loadSBML(int, string)

Load the sbml model contained in the string argument

void loadJarnac(int, string)

Load the Jarnac script model contained in the string argument

void changeInitialConditions (int, double[])

Load the initial conditions vector with a new vector

void setTimeStart (int, double)

Set the time start for the simulation

void setTimeEnd (int, double)

Set the time end for the simulation

void setNumPoints (int, int)

Set the number of output data points

void setSelectionList (int, {})

Sets the list of variables to return when calling simulate(), eg setSelectionList(handle, {'Time', 'S1', 'J0'

void reset (int)

Reset the model to it's initial conditions

double oneStep (int, double, double)

Carry out one step in the simulation. The method takes two arguments, the current time and the step size to use in the next integration step. The method returns the time at the new point. Usage: t = oneStep (modelHandle, t, 0.1)

double[][] simulate (int)

Carry out a simulation using a stiff ODE itegrator

double steadyState (int)

Compute the steady state, returns the sum fo squares indicating the quality of the solution

double[][] getReducedJacobian (int)

Get the current reduced jacobian matrix. This call will return the reduced matrix, that is dependent species have been removed

double[][] getFullJacobian (int)

Get the current full jacobian matrix.

double[][] evalModel (double, double, double[], double[])

Get the current state of the model, arg1 = time, arg2 = variable array, arg3 = parameter array

double getuCC (int, string, string)

Returns the unscaled control coefficient

double getCC (int, string, string)

Returns the scaled control coefficient

double getuEE (int, string, string)

Returns the unscaled elasticity coefficient

double getEE (int, string, string)

Returns the scaled elasticity coefficient

double[][] gillespie (int)

Carry out a simulation using the Gillespie method

void setValue (int, string, double)

Set the value of the named symbol, eg setValue (id, “ATP”, 1.2”)

double getValue (int, string)

Get the value of the named symbol, eg x = getValue (id, “ATP”)

double[] getReactionRates (int)

Get the reaction rates as a vector

double getReactionRate (int, int)

Get a particular reaction rate (id, ithReaction)

double[] getRatesOfChange (int)

Get the rates of change as a vector

{} getFloatingSpeciesNames(int)

Get the list of floating species names

double[] getFloatingSpeciesValues(int)

Get an array of floating species values

{} getReactionNames(int)

Get the list of reaction names

double[] getBoundarySpeciesValues ()

Get the list of boundary species values

{} getBoundarySpeciesNames ()

Get the list of boundary species names

int getNumLocalParameters(int)

Get the number of local parameters in the model

double[] getAllLocalParameterValues(int)

Get the list of local parameter values in the model

{} getAllLocalParameterNames(int)

Get the list of parameters in the model

int getNumFloatingSpecies(int)

Get the number of floating species

int getNumBoundarySpecies(int)

Get the number of boundary species

string getFloatingSpeciesName(int, int)

Get the ith floating species name

string getBoundarySpeciesName(int, int)

Get the ith boundary species name

{} getODEList (int)

Returns the model as a list of ODE equation strings

{} getRateLawList (int)

Returns the models' list of rate laws

double[][] getConservationLawArray (int)

Returns the conservation law array

double[][] getStoichiometryMatrix ()

Returns the stoichiometry matrix

double[][] getNrMatrix (int)

Returns the reduced stoichiometry matrix

double[][] getLinkMatrix (int)

Returns the link matrix

double[][] getUnScaledElasticityMatrix (int)

Returns the matrix of unscaled elasticities

int getNumReactions (int)

Returns the number of reaction in the current model

string getCapabilities (int)

Returns the simulators' capabilities

{} getIntegrationMethodList (int)

Returns the list simulator names

void setIntegrationMethod (int, string)

Sets the integration method

Service: sim

Jarnac simulation interface

string getName()

Returns the name of the module

string getVersion()

Returns the version number for this module

string getAuthor()

Returns the name of the author who wrote the module

string getDescription()

Returns a brief description of the module

string getDisplayName()

Returns a string suitable for display to a user

string getCopyright()

Returns the copyright notice, if any

string getURL()

Returns the URL for the module (if any)

void loadSBML(string)

Load the sbml model contained in the string argument

string getSBML(int)

Returns the current model as SBML, int arg is the level, 1 or 2

void loadJarnac(string)

Load the Jarnac script model contained in the string argument

void changeInitialConditions (double[])

Load the initial conditions vector with a new vector

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 output data points

void setSelectionList ({})

Sets the list of variables to return when calling simulate(), eg setSelectionList(handle, {'Time', 'S1', 'J0'

void reset ()

Reset the model to it's initial conditions

double oneStep (double, double)

Carry out one step in the simulation. The method takes two arguments, the current time and the step size to use in the next integration step. The method returns the time at the new point. Usage: t = oneStep (t, 0.1)

double[][] simulate()

Carry out a simulation using a stiff ODE itegrator

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

simulate (timeStart, timeEnd, numPoints)

void setFloatingSpeciesConcentrations(double[])

Sets all the floating species concentrations

void setFloatingSpeciesByIndex(int, double)

Sets the value of a floating species by it index value in the species array

void setBoundarySpeciesByIndex(int, double)

Sets the value of a floating species by it index value in the species array

double getFloatingSpeciesByIndex(int)

Get the concentration of floating species i

double getBoundarySpeciesByIndex(int)

Get the concentration of boundary species i

void setCompartmentByIndex(int,double)

Set compartment volume by index

double getCompartmentByIndex (int)

Get compartment volume by index

void setParameterByIndex(int, double)

Sets the value of a parameter by it index value in the parameter array

double[] getReactionRates()

Get the reaction rates as a vector

double[] getReactionRatesEx(double[])

Get the reaction rates given the floating species vector

double getReactionRate(int)

Get a particular reaction rate (ithReaction)

double[] getRatesOfChange()

Get the rates of change as a vector

double getRateOfChange(int)

Get a particular rates of change, indexed by species

double[] getRatesOfChangeEx (double[])

Get rates of change given the floating species vector

{} getRatesOfChangeNames()

Get the names of the symbols used to specify the rates of change

{} getFloatingSpeciesNames()

Get the list of floating species names

{} getSpeciesNames()

Get the list of floating species names

double[] getFloatingSpeciesConcentrations()

Get an array of floating species values

double[] getSpeciesValues()

Get an array of floating species values

{} getReactionNames()

Get the list of reaction names

double[] getBoundarySpeciesConcentrations()

Get the list of boundary species values

{} getBoundarySpeciesNames()

Get the list of boundary species names

void setBoundarySpeciesConcentrations(double[])

Set all boundary species concentrations

{} getAllLocalParameterNames()

Get the list of parameters in the model

{} getLocalParameterList()

Deprecated, use getAllLocalParameterNames

double[] getAllLocalParameterValues()

Get the list of local parameter values in the model

{} getLocalParameterNames(int)

Get the list of parameter names for reaction Id

double[] getLocalParameterValues(int)

Get the list of local parameter values in the model for reaction Id

void setLocalParameterByIndex(int, int, double)

Set a local parameter of reaction Id and parameter Id

double getLocalParameterByIndex(int, int)

Get value of local parameter of reaction Id and parameter Id

{} getGlobalParameterNames()

Get the list of global parameter

double[] getGlobalParameterValues()

Get the array of global parameters, returns zero in Jarnac

void setGlobalParameterByIndex (int, double)

Non-functional method, not applicable to Jarnac's internal model

double getGlobalParameterByIndex (int)

Non-functional method, not applicable to Jarnac's internal model

string getFloatingSpeciesName(int)

Get the ith floating species name

string getBoundarySpeciesName(int)

Get the ith boundary species name

int getNumReactions()

Returns the number of reaction in the current model

int getNumberOfReactions()

Returns the number of reaction in the current model

int getNumberOfCompartments()

Returns the number of compartments in the current model

{} getCompartmentNames()

Returns a list of compartment names in the current model

int getNumLocalParameters()

Get the number of local parameters in the model

int getNumberOfLocalParameters(int)

Get the number of local parameters in a particular reaction

int getNumberofGlobalParameters()

Will always return zero in Jarnac

int getNumFloatingSpecies()

Get the number of floating species

int getNumberOfFloatingSpecies()

Get the number of floating species

int getNumBoundarySpecies()

Get the number of boundary species

int getNumberOfBoundarySpecies()

Get the number of boundary species

int getNumIndependentSpecies()

Return the number of independent species

int getNumDependentSpecies()

Return the number of dependent species

double steadyState()

Compute the steady state, returns the sum fo squares indicating the quality of the solution

double[][] getReducedJacobian()

Get the current reduced jacobian matrix. This call will return the reduced matrix, that is dependent species have been removed

double[][] getJacobian()

Get the current reduced jacobian matrix. This call will return the reduced matrix, that is dependent species have been removed

double[][] getFullJacobian()

Get the current full jacobian matrix.

{} getODEList ()

Returns the model as a list of ODE equation strings

{} getRateLawList ()

Returns the models' list of rate laws

double[][] getConservationLawArray ()

Returns the conservation law array

void updateDependentSpecies ()

Updates the dependent species in the model

double[][] getStoichiometryMatrix ()

Returns the stoichiometry matrix

double[][] getNrMatrix ()

Returns the reduced stoichiometry matrix

double[][] getLinkMatrix ()

Returns the link matrix

double[][] getUnScaledElasticityMatrix ()

Returns the matrix of unscaled elasticities

double[][] getScaledElasticityMatrix ()

Returns the matrix of scaled elasticities

string getCapabilities ()

Gets the simulators' capabilities

void setCapabilities (string)

Sets the simulators' capabilities

double[][] evalModel(double, double[], double[])

Get the current state of the model, arg1 = time, arg2 = variable array, arg3 = parameter array

double getCC (string, string)

Returns the scaled control coefficient

double getuCC (string, string)

Returns the unscaled control coefficient

double getEE (string, string)

Returns the scaled elasticity coefficient

double getuEE (string, string)

Returns the unscaled elasticity coefficient

double getScaledFloatingSpeciesElasticity(string,string)

Returns the scaled elasticity coefficient for a given reaction and given species

double getUnscaledFloatingSpeciesElasticity(string,string)

Returns the unscaled elasticity coefficient for a given reaction and given species

double[][] gillespie()

Carry out a simulation using the Gillespie method

void setValue(string, double)

Set the value of the named symbol, eg setValue (“ATP”, 1.2”)

double getValue(string)

Get the value of the named symbol, eg x = getValue (“ATP”)

string eval(string)

evaluate a Jarnac script, eg eval (“print sin (30)”)

{} getIntegrationMethodList()

Returns the list simulator names

void setIntegrationMethod(string)

Sets the integration method

Service: biospiceSim

BioSPICE simulation interface

void loadSBMLString (string)

Load the sbml model contained in the string argument

void loadSBMLFile (string)

Load the sbml model contained in the string argument

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 output data points

void setSelectionList ({})

Sets the list of variables to return when calling simulate(), eg setSelectionList(handle, {'Time', 'S1', 'J0'

void reset ()

Reset the model to it's initial conditions

double oneStep (double, double)

Carry out one step in the simulation. The method takes two arguments, the current time and the step size to use in the next integration step. The method returns the time at the new point. Usage: t = oneStep (t, 0.1)

double[][] simulate ()

Carry out a simulation using a stiff ODE itegrator

void setValue (string, double)

Set the value of the named symbol, eg setValue (“ATP”, 1.2”)

double getValue (string)

Get the value of the named symbol, eg x = getValue (“ATP”)

{} getLocalParameterList()

Get the list of parameters in the model

{} getSpeciesNames()

Get the list of all floating species in the model

Service: biospiceAnalyzeSim

int initialize()
string getName()
string getDisplayName()
{} getInputTypes()
{} getOutputTypes()
{} getConfigurationParams()
{} analyze({})

Service: biospiceAnalyzeSS

int initialize()
string getName()
string getDisplayName()
{} getInputTypes()
{} getOutputTypes()
{} getConfigurationParams()
{} analyze({})

Service: mat

Matrix Library

double[][] getEigenValues (double [][])

Returns the eigenvalues for the matrix, first row holds the real components, second row the imaginary components

double[][] getInverse (double [][])

Returns the inverse of a matrix

Service: translator

Jarnac Translator

string getName()

Returns the name of the plugin

string getVersion()

Returns the verfsion number for the plugin

string getAuthor()

Returns the name of the plugin author

string getCopyright()

Returns the current licence

string getDescription()

Returns a description of the plugin

string getDisplayName()

Returns a display name string

string getURL()

Returns a web site address for the plugin

string translate(string)

Translates the argumen sbml string into Jarnac script

Service: asim

Provides Simulation Interface

string[] loadSBMLModel(string)

loads the sbml model

void doSteadyStateAnalysis(string[])

do steady state analysis

void doTimeBasedSimulation(double, double, int, string[])

do time based simulation

void stop()

stop simulation

void restart()

restart simulation

string[] optionsSupported()

Supported options

 
sbw/jarnac/api.txt · Last modified: 2007/03/15 00:42 by adeckard
 

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