"Tags" used in the SBML Test Suite

Tags are labels used to indicate properties of test cases in the SBML Test Suite. The labels are used in the NNNNN-model.m files describing every test case. Two different types of tags are used in the SBML Test Suite: component tags and test tags. For each test case, the relevant tags are listed after the componentTags: and testTags: fields, respectively, in the NNNNN-model.m file.

The following is an example of a model description file containing such tags:

(*
category:      Test
synopsis:      Basic single forward reaction with two species in one compartment
componentTags: Compartment, Species, Reaction, Parameter 
testTags:      InitialAmount, Concentration
testType:      TimeCourse
levels:        1.2, 2.1, 2.2, 2.3
generatedBy:   Analytic

The model contains one compartment called "compartment". There are two species called 
S1 and S2 and one parameter called k1. The model contains one reaction.
*)

The meaning of each possible tag is described below.

Component tags

Component tags describe the SBML elements that are present in the model. Most models are tagged with more than one component tag. (Readers may wonder whether these tags could be inferred simply by parsing the SBML content, and the answer is yes, they could. The tags are provided so that software systems can determine which components are used in each model without having to parse the model first. )

Test tags

Test tags may be combined in the same model. In fact, many of the SBML Test Suite test models are designed to explore escalating combinations of tests: one set of models may test a given tag, then another set of models may test that same tag plus a second tag, then a third model may test those two tags plus a third tag, in different combinations; and so on.

	Level:
Tag name	1	2	3	Meaning
0D-Compartment				Test interpretation of Compartment components that have a spatialDimensions attribute value of "0".
Amount				Test producing the output of Species components in terms of amounts (as opposed to concentrations or densities).
AssignedConstantStoichiometry				Test interpretation of a model in which the stoichiometry for one or more SpeciesReference components is assigned a value by a stoichiometryMath element (in L2), or by an initial assignment, assignment rule, or algebraic rule (in L3); however, the value does not change over the course of the simulation.
AssignedVariableStoichiometry				Test interpretation of a model in which the stoichiometry for one or more SpeciesReference components is assigned a value by a stoichiometryMath element (in L2) or by a rate rule, assignment rule, algebraic rule, or event (in L3), and the value is changed during the course of simulation.
BoundaryCondition				Test interpretation of Species components with different boundaryCondition attribute values.
Concentration				Test producing the output of Species components in terms of concentrations.
ConstantSpecies				Test interpretation of Species components whose constant attribute value is "true".
ConversionFactors				Test interpretation of Species or Model components that set values for their conversionFactor attributes.
EventIsNotPersistent				Test interpretation of Event components that contain Trigger subcomponents whose persistent attribute value is "false" and whose mathematical formulas (i.e., the trigger conditions) revert to "false" before execution.
EventIsPersistent				Test interpretation of Event components that contain Trigger subcomponents whose persistent attribute value is "true" (in L3) or whose triggers are persistent by definition (L2), and whose mathematical formulas (i.e., the trigger conditions) revert to "false" before execution.
EventT0Firing				Test interpretation of Event components whose Trigger evaluates to "true" when time t = 0, which means that whether it is allowed to fire then (possible in L3; impossible in L2) makes a difference to the output of the simulation.
EventUsesAssignmentTimeValues				Test interpretation of Event components in which calculations for the EventAssignment subcomponents are meant to be done at the moment of event execution.
EventUsesTriggerTimeValues				Test interpretation of Event components in which calculations for the EventAssignment subcomponents are meant to be done at the moment of event triggering.
FastReaction				Test interpretation of Reaction components whose fast attribute value is "true".
HasOnlySubstanceUnits				Test interpretation of Species components whose hasOnlySubstanceUnits attribute value is "true".
InitialValueReassigned				Test interpretation of models where a component has an initial value declared (size, initialAmount, value, stoichiometry, etc.), but this declared value is different from the value assigned to the component by another SBML construct (such as, e.g., InitialAssignment in Levels 2–3).
LocalParameters				Test interpretation of Reaction components that have local parameter declarations within their KineticLaw subcomponents.
MultiCompartment				Test interpretation of Model components with more than one Compartment component.
NonConstantCompartment				Test interpretation of Compartment components whose size changes during the course of simulation.
NonConstantParameter				Test interpretation of Parameter components whose value changes during the course of simulation.
NonUnityCompartment				Test interpretation of Compartment components whose size is not numerically equal to "1". (Note that if the NonConstantCompartment tag is also present, then the value varies during simulation and may be equal to "1" at some point during simulation.)
NonUnityStoichiometry				Test interpretation of SpeciesReference subcomponents in Reactions where the SpeciesReference stoichiometry is not numerically equal to "1". (Note that if the NonConstantParameter tag is also present, then the value varies during simulation and may be equal to "1" at some point during simulation.)
RandomEventExecution				Test interpretation of models containing multiple Event components each of which execute at the same moment, and whose Priority subcomponents are identical; this should have the effect that the order of event execution is chosen at random at simulation time.
ReversibleReaction				Test interpretation of models containing Reaction components whose reversible attribute values are "true", and whose KineticLaw evaluates to being negative for at least part of the simulation.
SpeciesReferenceInMath				The identifier of a SpeciesReference object is used in the <math> element of at least one SBML object in the model.