SIMULATION

The functions allow users to simulate SBML Models.

Function are:

[analysis] = AnalyseSpecies(SBMLModel)

Takes

1. SBMLModel, an SBML Model structure

Returns

1. a structure detailing the species and how they are manipulated within the model

EXAMPLE:

     Using the model from toolbox/Test/test-data/algebraicRules.xml

        analysis = AnalyseSpecies(m)

        analysis = 

        1x5 struct array with fields:
            Name
            constant
            boundaryCondition
            initialValue
            hasAmountOnly
            isConcentration
            compartment
            ChangedByReaction
            KineticLaw
            ChangedByRateRule
            RateRule
            ChangedByAssignmentRule
            AssignmentRule
            InAlgebraicRule
            AlgebraicRule
            ConvertedToAssignRule
            ConvertedRule

        analysis(1) = 


                               Name: {'S1'}
                           constant: 0
                  boundaryCondition: 0
                       initialValue: 0.0300
                      hasAmountOnly: 0
                    isConcentration: 0
                        compartment: 'compartment'
                  ChangedByReaction: 1
                         KineticLaw: {' - (k*S1)'}
                  ChangedByRateRule: 0
                           RateRule: ''
            ChangedByAssignmentRule: 0
                     AssignmentRule: ''
                    InAlgebraicRule: 1
                      AlgebraicRule: {{1x1 cell}}
              ConvertedToAssignRule: 0
                      ConvertedRule: ''

[analysis] = AnalyseVaryingParameters(SBMLModel)

Takes

1. SBMLModel, an SBML Model structure

Returns

1. a structure detailing any parameters that are not constant and how they are manipulated within the model

EXAMPLE:

     Using the model from toolbox/Test/test-data/algebraicRules.xml

       analysis = AnalyseVaryingParameters(m)

       analysis = 
                   Name: {'s2'}
           initialValue: 4
      ChangedByRateRule: 0
               RateRule: ''
ChangedByAssignmentRule: 0
         AssignmentRule: ''
        InAlgebraicRule: 1
          AlgebraicRule: {{1x1 cell}}
  ConvertedToAssignRule: 1
          ConvertedRule: '-(-S2-S3)'

elements = DealWithPiecewise(formula)

Takes

1. formula, a string representation of a math expression that contains the MathML piecewise function

Returns

1. an array of the three components of the piecewise function

EXAMPLE:

      elements = DealWithPiecewise('piecewise(le(s2,4),1.5,0.05)')

               =  'le(s2,4)'  '1.5'   '0.05'

NOTE: The function cannot deal with a piecewise statement with more than three elements.

elements = GetArgumentsFromLambdaFunction(formula)

Takes

1. formula, a string representation of a math expression that contains the MathML lambda function

Returns

1. an array of the components of the lambda function

EXAMPLE:

      elements = GetArgumentsFromLambdaFunction('lambda(x, x+0.5)')

               =  'x'  'x+0.5'   

      elements = GetArgumentsFromLambdaFunction('lambda(x, y, x + y)')

               =  'x'  'y'    'x+y'

OutputODEFunction

NOTE: This function is deprecated. Use SolveODEFunction instead.

SolveODEFunction(varargin)

Takes

1. a MATLAB_SBML model structure (required argument)
2. time limit (default = 10)
3. number of time steps (default lets the solver decide)
4. a flag to indicate whether to output species values in amount/concentration 1 amount, 0 concentration (default)
5. a flag to indicate whether to output the simulation data as a comma separated variable (csv) file 1 output 0 no output (default)
6. a filename (this is needed if WriteODEFunction was used with a filename)

Returns

1. an array of time values
2. an array of the values of variables at each time point; species will be in concentration or amount as specified by input arguments

Outputs

1. a file 'name.csv' with the data results (if the flag to output such a file is set to 1.

NOTE: the results are generated using ode45 solver (MATLAB) or lsode (Octave)

WriteEventAssignmentFunction(SBMLModel, name)

Takes

1. SBMLModel, an SBML Model structure
2. name, a string representing the name of the ode function being used

Outputs

1. a file 'name_eventAssign.m' defining a function that assigns values following an event (for use with the event option of MATLABs ode solvers)

NOTE: This function is called from WriteODEFunction when a model with events is encountered.

WriteEventHandlerFunction(SBMLModel, name)

Takes

1. SBMLModel, an SBML Model structure
2. name, a string representing the name of the ode function being used

Outputs

1. a file 'name_events.m' defining a function that tests whether events have been triggered (for use with the event option of MATLABs ode solvers)

NOTE: This function is called from WriteODEFunction when a model with events is encountered.

WriteODEFunction(SBMLModel, name(optional))

Takes

1. SBMLModel, an SBML Model structure
2. name, an optional string representing the name of the ode function to be used

Outputs

1. a file 'name.m' defining a function that defines the ode equations of the model for use with the ode solvers (if no name supplied the model id will be used)