Computing initial values for pools of instances

In SBML Level 3 Version 1, InitialAssignments are used to assign initial values to variables of a model, that are Compartments, Species, SpeciesReference, or global Parameters. In order to assign the value of a specific type of species, InitialAssignments in multi Version 1 also contain an element SpeciesTypeInstanceChange. The assignment sets the initial quantity of instances that fulfill a certain selection using the mathematical expression provided. The value provided by the InitialAssignment overides the value provided by the attributes initialAmount or initialConcentration of the relevant SpeciesTypeInstance.

InitialAssignment and all the associated classes of multi version 1.

InitialAssignment

In order to assign the initial values to entity subpools, defined by specific state and connectivity, the element InitialAssignment of SBML Level 3 Version 1 core is linked to a SpeciesTypeInstanceChange.

Defintion of the extended version of InitialAssignment and its relation with SBase.

SpeciesTypeInstanceChange

As all elements derived from SBase, a SpeciesTypeInstanceChange can link to Notes and Annotation, and carry a metaid , and an sboTerm . It targets a SpeciesTypeInstance through its speciesTypeInstance attribute. The change is computed using a MathML construct, as is always the case in SBML Level 3 Version 1.

Defintion of the extended version of SpeciesTypeInstanceChange and its relation with SBase.

Complete example of an initial assignment

The following example presents the assignment of the initial value for the subpool of species1 defined as speciesTypeInstance1. This value is computed as the product of the parameters x and y, defined elsewhere.

Note the empty Math, used when the software is unable to use the package multi Version 1.

<species id="species1"
         boundaryCondition="false" 
         hasOnlySubstanceUnit="false" 
         constant="false"
         compartment="compartment1" 
         initialAmount="1000"
         xmlns:multi="http://www.sbml.org/sbml/level3/version1/multi/version1"
         multi:speciesType="speciesType1" >
  <multi:listOfSpeciesTypeInstances>
    <multi:SpeciesTypeInstance id="speciesTypeInstance1" initialAmount="1">
      <multi:listOfSelectorReferences>
        <multi:selectorReference selector="selector1">
      </multi:listOfSelectorReferences>
    </multi:speciesTypeInstance>
  </multi:listOfSpeciesTypeInstances>
</species>

<initialAssignement symbol="species1">
  <multi:speciesTypeInstanceChange speciesTypeInstance="speciesTypeInstance1">
    <math xmlns="http://www.w3.org/1998/Math/MathML">
      <apply>
        <times/>
        <ci> x </ci>
        <ci> y </ci>
      </apply>
    </math>
  </multi:speciesTypeInstanceChange>
  <math xmlns="http://www.w3.org/1998/Math/MathML" />
</initialAssignement>

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