Multi-simulation interface, most calls require the model handle as the first argument
Start a new model instance, returns model handle
Destroy a model given it's model handle
Load the sbml model contained in the string argument
Load the Jarnac script model contained in the string argument
Load the initial conditions vector with a new vector
Set the time start for the simulation
Set the time end for the simulation
Set the number of output data points
Sets the list of variables to return when calling simulate(), eg setSelectionList(handle, {'Time', 'S1', 'J0'
Reset the model to it's initial conditions
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)
Carry out a simulation using a stiff ODE itegrator
Compute the steady state, returns the sum fo squares indicating the quality of the solution
Get the current reduced jacobian matrix. This call will return the reduced matrix, that is dependent species have been removed
Get the current full jacobian matrix.
Get the current state of the model, arg1 = time, arg2 = variable array, arg3 = parameter array
Returns the unscaled control coefficient
Returns the scaled control coefficient
Returns the unscaled elasticity coefficient
Returns the scaled elasticity coefficient
Carry out a simulation using the Gillespie method
Set the value of the named symbol, eg setValue (id, “ATP”, 1.2”)
Get the value of the named symbol, eg x = getValue (id, “ATP”)
Get the reaction rates as a vector
Get a particular reaction rate (id, ithReaction)
Get the rates of change as a vector
Get the list of floating species names
Get an array of floating species values
Get the list of reaction names
Get the list of boundary species values
Get the list of boundary species names
Get the number of local parameters in the model
Get the list of local parameter values in the model
Get the list of parameters in the model
Get the number of floating species
Get the number of boundary species
Get the ith floating species name
Get the ith boundary species name
Returns the model as a list of ODE equation strings
Returns the models' list of rate laws
Returns the conservation law array
Returns the stoichiometry matrix
Returns the reduced stoichiometry matrix
Returns the matrix of unscaled elasticities
Returns the number of reaction in the current model
Returns the simulators' capabilities
Returns the list simulator names
Sets the integration method
Jarnac simulation interface
Returns the name of the module
Returns the version number for this module
Returns the name of the author who wrote the module
Returns a brief description of the module
Returns a string suitable for display to a user
Returns the copyright notice, if any
Returns the URL for the module (if any)
Load the sbml model contained in the string argument
Returns the current model as SBML, int arg is the level, 1 or 2
Load the Jarnac script model contained in the string argument
Load the initial conditions vector with a new vector
Set the time start for the simulation
Set the time end for the simulation
Set the number of output data points
Sets the list of variables to return when calling simulate(), eg setSelectionList(handle, {'Time', 'S1', 'J0'
Reset the model to it's initial conditions
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)
Carry out a simulation using a stiff ODE itegrator
simulate (timeStart, timeEnd, numPoints)
Sets all the floating species concentrations
Sets the value of a floating species by it index value in the species array
Sets the value of a floating species by it index value in the species array
Get the concentration of floating species i
Get the concentration of boundary species i
Set compartment volume by index
Get compartment volume by index
Sets the value of a parameter by it index value in the parameter array
Get the reaction rates as a vector
Get the reaction rates given the floating species vector
Get a particular reaction rate (ithReaction)
Get the rates of change as a vector
Get a particular rates of change, indexed by species
Get rates of change given the floating species vector
Get the names of the symbols used to specify the rates of change
Get the list of floating species names
Get the list of floating species names
Get an array of floating species values
Get an array of floating species values
Get the list of reaction names
Get the list of boundary species values
Get the list of boundary species names
Set all boundary species concentrations
Get the list of parameters in the model
Deprecated, use getAllLocalParameterNames
Get the list of local parameter values in the model
Get the list of parameter names for reaction Id
Get the list of local parameter values in the model for reaction Id
Set a local parameter of reaction Id and parameter Id
Get value of local parameter of reaction Id and parameter Id
Get the list of global parameter
Get the array of global parameters, returns zero in Jarnac
Non-functional method, not applicable to Jarnac's internal model
Non-functional method, not applicable to Jarnac's internal model
Get the ith floating species name
Get the ith boundary species name
Returns the number of reaction in the current model
Returns the number of reaction in the current model
Returns the number of compartments in the current model
Returns a list of compartment names in the current model
Get the number of local parameters in the model
Get the number of local parameters in a particular reaction
Will always return zero in Jarnac
Get the number of floating species
Get the number of floating species
Get the number of boundary species
Get the number of boundary species
Return the number of independent species
Return the number of dependent species
Compute the steady state, returns the sum fo squares indicating the quality of the solution
Get the current reduced jacobian matrix. This call will return the reduced matrix, that is dependent species have been removed
Get the current reduced jacobian matrix. This call will return the reduced matrix, that is dependent species have been removed
Get the current full jacobian matrix.
Returns the model as a list of ODE equation strings
Returns the models' list of rate laws
Returns the conservation law array
Updates the dependent species in the model
Returns the stoichiometry matrix
Returns the reduced stoichiometry matrix
Returns the matrix of unscaled elasticities
Returns the matrix of scaled elasticities
Gets the simulators' capabilities
Sets the simulators' capabilities
Get the current state of the model, arg1 = time, arg2 = variable array, arg3 = parameter array
Returns the scaled control coefficient
Returns the unscaled control coefficient
Returns the scaled elasticity coefficient
Returns the unscaled elasticity coefficient
Returns the scaled elasticity coefficient for a given reaction and given species
Returns the unscaled elasticity coefficient for a given reaction and given species
Carry out a simulation using the Gillespie method
Set the value of the named symbol, eg setValue (“ATP”, 1.2”)
Get the value of the named symbol, eg x = getValue (“ATP”)
evaluate a Jarnac script, eg eval (“print sin (30)”)
Returns the list simulator names
Sets the integration method
BioSPICE simulation interface
Load the sbml model contained in the string argument
Load the sbml model contained in the string argument
Set the time start for the simulation
Set the time end for the simulation
Set the number of output data points
Sets the list of variables to return when calling simulate(), eg setSelectionList(handle, {'Time', 'S1', 'J0'
Reset the model to it's initial conditions
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)
Carry out a simulation using a stiff ODE itegrator
Set the value of the named symbol, eg setValue (“ATP”, 1.2”)
Get the value of the named symbol, eg x = getValue (“ATP”)
Get the list of parameters in the model
Get the list of all floating species in the model
Returns the eigenvalues for the matrix, first row holds the real components, second row the imaginary components
Returns the inverse of a matrix
Returns the name of the plugin
Returns the verfsion number for the plugin
Returns the name of the plugin author
Returns the current licence
Returns a description of the plugin
Returns a display name string
Returns a web site address for the plugin
Translates the argumen sbml string into Jarnac script
Provides Simulation Interface
