Syntax and semantics

The proposal for extending SBML to carry the information for multistate multicomponent species relies on the extension of the following core SBML elements: Species, InitialAssignment, Rule, Reaction, SimpleSpeciesReference, EventAssignment. In addition, the multistate multi-component package requires the creation of new main elements: SpeciesType, Selector.

A software that does not understand multi Version 1 can ignore entirely all elements in the corresponding namespace. The remaining SBML model is a valid SBML Level 3 Version 1 core.

In the UML diagrams contained in this specification, the elements and attributes specific to the package multi are drawn in red, while the elements and attributes belonging to SBML core are drawn in black. Not all of the latter are drawn, but only the ones needed to "plug" the package multi. Please consult the specification of the core for a deeper understanding of SBML at large.

Extension of the model element

In order to encode the structures needed to define and use multistate and multi-component complexes, the element model is extended to be linked to a list of SpeciesTypes and a list of Selectors.

Example of a molecular entity carrying a multi-valued variable and containing another entity.

<model xmlns:multi="http://www.sbml.org/sbml/level3/version1/multi/version1">
  
  <!-- some compartments -->
  
  <multi:listOfSpeciesTypes>
    <!-- some species types -->
  </multi:listOfSpeciesTypes>

  <multi:listOfSelectors>
    <!-- some selectors -->
  </multi:listOfSelectors>

  <!-- some species, initialAssignments, rules, reactions, events -->
  
</model>

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