SBML.org — the global portal for all things SBML

TestTags Descriptions

The testTags used to categorize test cases relate to SBML components and their attributes as detailed in the SBML Specifications.

TestTags with relevant component/attribute
TestTag Component Attribute
2D-Compartment Compartment spatialDimensions
1D-Compartment Compartment spatialDimensions
0D-Compartment Compartment spatialDimensions
NonConstantCompartment Compartment constant
NonUnityCompartment Compartment size/volume
InitialAmount Species initialAmount
InitialConcentration Species initialConcentration
HasOnlySubstanceUnits Species hasOnlySubstanceUnits
BoundaryCondition Species boundaryCondition
ConstantSpecies Species constant
MassUnits Species substanceUnits
NonConstantParameter Parameter constant
FastReaction Reaction fast
ReversibleReaction Reaction reversible
NonUnityStoichiometry SpeciesReference stoichiometry
StoichiometryMath SpeciesReference stoichiometryMath
LocalParameters KineticLaw listOfParameters
CSymbolTime Various math
CSymbolDelay Various math
Units Various unit
MultiCompartment Model listOfCompartments

nD-Compartment

Component Attribute SBML Specification Reference
Compartment spatialDimensions
Level Section
L2V3 4.7.3
L2V2 4.7.3
L2V1 4.5.2
L1V2 N/A

A Compartment object has an optional attribute spatialDimensions, whose value must be a positive integer indicating the number of spatial dimensions possessed by the compartment. Permissible values are 0, 1, 2 and 3 (default). Note that the number of spatial dimensions possessed by a compartment affects certain aspects of the compartment’s size and units.

The TestSuite provides cases where the testTags 2D-Compartment, 1D-Compartment and 0D-Compartment indicate the value of the spatialDimensions attribute. The value of spatialDimensions defaults to 3 for any cases without one of these testTags.

NonConstantCompartment

Component Attribute SBML Specification Reference
Compartment constant
Level Section
L2V3 4.7.6
L2V2 4.7.6
L2V1 4.5.3
L1V2 N/A

A Compartment also has an optional boolean attribute constant that indicates whether the compartment’s size stays constant or can vary during a simulation. A value of false indicates the compartment’s size can be changed by other constructs in SBML. A value of true (default) indicates the compartment’s size cannot be changed by any other construct except InitialAssignment.

The TestSuite provides cases where the testTag NonConstantCompartment indicates that the size of the compartment is being changed during simulation for example by a RateRule.

Note that although the constant attribute is not explicitly present in SBML Level 1 it is possible to create models where the compartment's volume is either fixed or varying.

NonUnityCompartment

Component Attribute SBML Specification Reference
Compartment size/volume
Level Section
L2V3 4.7.4
L2V2 4.7.4
L2V1 4.5.3
L1V2 4.3

A Compartment has an optional floating-point attribute size, representing the initial total size of the compartment. The size may be a volume (if the compartment is a three-dimensional one), or it may be an area (if the compartment is two-dimensional), or a length (if the compartment is one-dimensional).

Note that in SBML Level 1 the corresponding attribute was called volume; since all compartments were considered to be three-dimensional; and had a default value of 1.

The TestSuite provides cases where the testTag NonUnityCompartment indicates that the size of the compartment is not 1.

InitialAmount

Component Attribute SBML Specification Reference
Species initialAmount
Level Section
L2V3 4.8.4
L2V2 4.8.4
L2V1 4.6.3
L1V2 4.4

A Species has an optional floating-point attribute initialAmount representing the initial amount of the species in the compartment where the species is located.

The TestSuite provides cases where the testTag InitialAmount indicates that this attribute has been used to set the initial quantities of the species. This make it easier to use the model in a discrete stochastic simulator, but (as per usual SBML principles) the species symbols represent their values in concentration units where they appear in expressions.

InitialConcentration

Component Attribute SBML Specification Reference
Species initialConcentration
Level Section
L2V3 4.8.4
L2V2 4.8.4
L2V1 4.6.3
L1V2 N/A

A Species has an optional floating-point attribute initialConcentration representing the initial concentration of the species in the compartment where the species is located.

The TestSuite provides cases where the testTag InitialConcentration indicates that this attribute has been used to set the initial quantities of the species.

HasOnlySubstanceUnits

Component Attribute SBML Specification Reference
Species hasOnlySubstanceUnits
Level Section
L2V3 4.8.5
L2V2 4.8.5
L2V1 4.6.4
L1V2 N/A

A Species has optional boolean attribute hasOnlySubstanceUnits that defaults to false. This attribute’s role is to indicate whether the units of the species, when the species identifier appears in mathematical formulas, are intended to be concentration or amount. A value of true implies that the units are those of amount; false implies units of concentration.

The TestSuite provides cases with the testTag HasOnlySubstanceUnits that means that the 'hasOnlySubstanceUnits' attribute has been set as true, thus indicating that the species identifier should be treated as an amount when it appears in a mathematical expression. Cases without this testTag assume the attribute defaults to false.

BoundaryCondition

Component Attribute SBML Specification Reference
Species boundaryCondition
Level Section
L2V3 4.8.6
L2V2 4.8.6
L2V1 4.6.6
L1V2 4.4

A Species object has an optional boolean attribute boundaryCondition that defaults to false. Setting this attribute to true indicates that the given species’ quantity is not determined by the set of reactions even when that species occurs as a product or reactant; i.e., the species is on the boundary of the reaction system, and its quantity is not determined by the reactions.

The TestSuite provides cases where the testTag BoundaryCondition indicates that the model contains species which are reactants or products within reactions and have been labeled as being on the boundary. Cases without this tag are models where the attribute defaults to false.

ConstantSpecies

Component Attribute SBML Specification Reference
Species constant
Level Section
L2V3 4.8.6
L2V2 4.8.6
L2V1 4.6.5
L1V2 N/A

A Species has optional boolean attribute constant that defaults to false and indicates whether the species’ quantity can be changed at all, regardless of whether by reactions, rules, or constructs other than InitialAssignment.

The TestSuite provides cases with the testTag ConstantSpecies where the constant attribute on a species has been set to true. Cases without this tag are models where this attribute defaults to false.

MassUnits

Component Attribute SBML Specification Reference
Species substanceUnits
Level Section
L2V3 4.4.3
L2V2 4.4.3
L2V1 -
L1V2 -

Mass as an allowable substance unit was introduced in SBML L2V2.

NonConstantParameter

Component Attribute SBML Specification Reference
Parameter constant
Level Section
L2V3 4.9.4
L2V2 4.9.4
L2V1 4.7.4
L1V2 N/A

A Parameter has an optional boolean attribute constant that indicates whether the parameter's value stays constant or can vary during a simulation. A value of false indicates the parameter's value can be changed by other constructs in SBML. A value of true (default) indicates the parameter's value cannot be changed by any other construct except InitialAssignment.

The TestSuite provides cases where the testTag NonConstantParameter indicates that the value of a parameter is being changed during simulation for example by a RateRule.

Note that although the constant attribute is not explicitly present in SBML Level 1 it is possible to create models where the parameter's value is either fixed or varying.

FastReaction

Component Attribute SBML Specification Reference
Reaction fast
Level Section
L2V3 4.13.1
L2V2 4.13.1
L2V1 4.9.4
L1V2 4.7

A Reaction has an optional boolean attribute fast which defaults to false. When a model contains true values for fast on any of its reactions, it is an indication that the creator of the model is distinguishing different time scales of reactions in the system. The set of reactions having fast = true should be assumed to be operating on a time scale significantly faster than the other reactions (the slow reactions).

ReversibleReaction

Component Attribute SBML Specification Reference
Reaction reversible
Level Section
L2V3 4.13.1
L2V2 4.13.1
L2V1 4.9.3
L1V2 4.7

A Reaction has an optional boolean attribute reversible that indicates whether the reaction is reversible. The default is true. Mathematically, the reversible attribute on Reaction has no impact on the construction of the equations giving the overall rates of change of each species quantity in a model.

The TestSuite provides cases where the testTag ReversibleReaction indicates that one or more of the reactions have the reversible attribute set to true. Cases without this tag will only contain reactions were the reversible attribute is false.

NonUnityStoichiometry

Component Attribute SBML Specification Reference
SpeciesReference stoichiometry
Level Section
L2V3 4.13.3
L2V2 4.13.3
L2V1 4.9.5
L1V2 4.7.1

A SpeciesReference object has an optional floating-point attribute stoichiometry that specifies the stoichiometry of either products or reactants. The value should be greater than 0 and defaults to 1.

The TestSuite provides cases where the testTag NonUnityStoichiometry indicates that the stoichiometry of one or more products or reactants is not 1.

StoichiometryMath

Component Attribute SBML Specification Reference
SpeciesReference stoichiometryMath
Level Section
L2V3 4.13.3
L2V2 4.13.3
L2V1 4.9.5
L1V2 N/A

A SpeciesReference object has an optional element stoichiometryMath that implements the stoichiometry of the object as a MathML expression.

The TestSuite provides cases where the testTag StoichiometryMath indicates that the stoichiometry of one or more reactants or products must be calculated using the stoichiometryMath element.

LocalParameters

Component Attribute SBML Specification Reference
KineticLaw listOfParameters
Level Section
L2V3 4.13.5
L2V2 4.13.5
L2V1 4.9.7
L1V2 4.7.2

An instance of KineticLaw can contain a list of one or more Parameter objects which define new parameters whose identifiers can be used in the math formula. Reactions introduce local namespaces for parameter identifiers, and within a KineticLaw object, a local Parameter whose identifier is identical to a global identifier defined in the model takes precedence over the value associated with the global identifier.

The TestSuite provides cases where the testTag LocalParameters indicates that one or more kinetic laws within the model declare local parameters, whose identifiers may shadow global identifiers.

CSymbolTime

Component Attribute SBML Specification Reference
Various math
Level Section
L2V3 3.4.6
L2V2 3.5.5
L2V1 3.6.4
L1V2 N/A

SBML Level 2 uses the MathML csymbol element to denote certain built-in mathematical entities without introducing reserved names into the component identifier namespace. The csymbol time with the definitionURL http://www.sbml.org/sbml/symbols/time represents the current simulation time.

CSymbolDelay

Component Attribute SBML Specification Reference
Various math
Level Section
L2V3 3.4.6
L2V2 3.5.5
L2V1 3.6.4
L1V2 N/A

SBML Level 2 uses the MathML csymbol element to denote certain built-in mathematical entities without introducing reserved names into the component identifier namespace. The csymbol delay with the definitionURL http://www.sbml.org/sbml/symbols/delay represents a delay function.

Units

Component Attribute SBML Specification Reference
Various unit
Level Section
L2V3 3.4.10
L2V2 3.4.10
L2V1 -*
L1V2 -*

Implicit unit conversions do not exist in SBML.

MultiCompartment

Component Attribute SBML Specification Reference
Model listOfCompartments
Level Section
L2V3 7.7
L2V2 7.7
L2V1 5.6
L1V2 -*

A Model object may contain more than one Compartment. A Reaction object can define reactions between species contained within one compartment or within multiple compartments.

-* A missing reference implies that this situation was not explicitly discussed within the specification; it is however possible to create a model that tests the given tag.


Retrieved from "http://sbml.org/Software/SBML_Test_Suite/TestTags_Descriptions"

This page was last modified 07:14, 1 April 2010.



Please use our issue tracking system for any questions or suggestions about this website. This page was last modified 07:14, 1 April 2010.