sbmltoolbox 4.1.0-2 / usr / share / doc / sbmltoolbox / html / simulation.html

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<h3>SIMULATION</h3>

<p>The functions allow users to simulate SBML Models.</p>

<p>Function are:</p>

<hr>

<h4>[analysis] = AnalyseSpecies(SBMLModel)</h4>

<p>Takes</p>

<ol>
<li>SBMLModel, an SBML Model structure</li>
</ol>

<p>Returns</p>

<ol>
<li>a structure detailing the species and how they are manipulated 
          within the model</li>
</ol>

<p><em>EXAMPLE:</em></p>

<pre><code>     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: ''
</code></pre>

<hr>

<h4>[analysis] = AnalyseVaryingParameters(SBMLModel)</h4>

<p>Takes</p>

<ol>
<li>SBMLModel, an SBML Model structure</li>
</ol>

<p>Returns</p>

<ol>
<li>a structure detailing any parameters that are not constant and how they are manipulated 
          within the model</li>
</ol>

<p><em>EXAMPLE:</em></p>

<pre><code>     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)'
</code></pre>

<hr>

<h4>elements = DealWithPiecewise(formula)</h4>

<p>Takes </p>

<ol>
<li>formula, a string representation of a math expression that contains the MathML piecewise function </li>
</ol>

<p>Returns </p>

<ol>
<li>an array of the three components of the piecewise function</li>
</ol>

<p><em>EXAMPLE:</em></p>

<pre><code>      elements = DealWithPiecewise('piecewise(le(s2,4),1.5,0.05)')

               =  'le(s2,4)'  '1.5'   '0.05'
</code></pre>

<p><em>NOTE:</em> The function cannot deal with a piecewise statement with more
than three elements.</p>

<hr>

<h4>elements = GetArgumentsFromLambdaFunction(formula)</h4>

<p>Takes</p>

<ol>
<li>formula, a string representation of a math expression that contains the MathML lambda function </li>
</ol>

<p>Returns </p>

<ol>
<li>an array of the components of the lambda function</li>
</ol>

<p><em>EXAMPLE:</em></p>

<pre><code>      elements = GetArgumentsFromLambdaFunction('lambda(x, x+0.5)')

               =  'x'  'x+0.5'   

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

               =  'x'  'y'    'x+y'
</code></pre>

<hr>

<h4>OutputODEFunction</h4>

<p><em>NOTE:</em> This function is deprecated. Use SolveODEFunction instead. </p>

<hr>

<h4>SolveODEFunction(varargin)</h4>

<p>Takes </p>

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

<p>Returns</p>

<ol>
<li>an array of time values</li>
<li>an array of the values of variables at each time point; species will
be in concentration or amount as specified by input arguments</li>
</ol>

<p>Outputs </p>

<ol>
<li>a file 'name.csv' with the data results (if the flag to output such a
file is set to 1.</li>
</ol>

<p><em>NOTE:</em> the results are generated using ode45 solver (MATLAB) or lsode
(Octave)</p>

<hr>

<h4>WriteEventAssignmentFunction(SBMLModel, name)</h4>

<p>Takes </p>

<ol>
<li>SBMLModel, an SBML Model structure</li>
<li>name, a string representing the name of the ode function being used</li>
</ol>

<p>Outputs </p>

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

<p><em>NOTE:</em> This function is called from WriteODEFunction when a model with
 events is encountered.</p>

<hr>

<h4>WriteEventHandlerFunction(SBMLModel, name)</h4>

<p>Takes </p>

<ol>
<li>SBMLModel, an SBML Model structure</li>
<li>name, a string representing the name of the ode function being used</li>
</ol>

<p>Outputs </p>

<ol>
<li>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)</li>
</ol>

<p><em>NOTE:</em> This function is called from WriteODEFunction when a model with
 events is encountered.</p>

<hr>

<h4>WriteODEFunction(SBMLModel, name(optional))</h4>

<p>Takes </p>

<ol>
<li>SBMLModel, an SBML Model structure</li>
<li>name, an optional string representing the name of the ode function to be used</li>
</ol>

<p>Outputs </p>

<ol>
<li>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)</li>
</ol>

<hr>