Reference
Every element type a report shows, the attributes of the elements and the fields the report adds. The pages are generated from the glossary of the repository, which is also the source of the tooltips of the application.
The link kinds explain how the elements of a report reference each other, the report concepts explain what the report computes on top of the model, and the data types explain the values its attributes and its fields carry.
Core
element
meaning
SBase the attributes every element of an SBML model carries
SBMLDocument the container of an SBML file, with its level, version and packages
Model the container of everything a model is made of
FunctionDefinition a named function which the mathematics of the model can call
UnitDefinition a named unit built from the base units of SBML
Compartment a bounded space in which species are located
Species a pool of a chemical entity in a compartment
Parameter a named value which the mathematics of the model can use
InitialAssignment a formula which computes the value of an element at the start of the simulation
AssignmentRule a formula which holds at every moment of the simulation
RateRule a formula which gives the rate of change of an element
AlgebraicRule an equation which has to hold at every moment of the simulation
Constraint a condition which a valid simulation of the model has to satisfy
Reaction a process which changes the quantities of species
Event an instantaneous change of the model when a condition becomes true
SpeciesReference the participation of a species in a reaction as a reactant or a product
ModifierSpeciesReference the participation of a species in a reaction as a modifier
KineticLaw the formula which gives the speed of a reaction
LocalParameter a named value which only one kinetic law uses
Trigger the condition of an event, whose change from false to true fires it
Priority the formula which orders an event against the other events of the same moment
Delay the formula which gives the time between the trigger of an event and its execution
EventAssignment the new value an event gives to one element of the model
ListOf a list of a model or of an element which states something of its own
Hierarchical models (comp)
element
meaning
Hierarchical Model Composition (comp) the package which builds a model out of other models
ExternalModelDefinition a model of another SBML file which this document can instantiate
Submodel the instantiation of another model inside this model
Port an element of the model which other models are meant to connect to
SBaseRef a link of a chain which reaches into a submodel of a submodel
Deletion an element which is removed from a submodel before it is instantiated
ReplacedElement an element of a submodel which the element carrying it takes the place of
ReplacedBy the element of a submodel which takes the place of the element carrying it
Flux balance constraints (fbc)
element
meaning
Flux Balance Constraints (fbc) the package which describes a constraint based model
GeneProduct a gene or one of its products which the reactions of the model depend on
Objective the function a flux balance analysis maximises or minimises
FluxObjective one term of an objective: a reaction weighted by a coefficient
FluxBound a constraint on the flux of a reaction, as fbc Version 1 writes it
UserDefinedConstraint a constraint over a combination of fluxes and parameters, added in Version 3
UserDefinedConstraintComponent one weighted variable of a user defined constraint
GeneProductAssociation the genes a reaction needs, as the tree of operators over them
And the associations below it are all needed at once
Or one of the associations below it suffices
GeneProductRef the leaf of an association: one gene product the reaction depends on
Qualitative models (qual)
element
meaning
Qualitative Models (qual) the package which describes a model whose entities carry a level
QualitativeSpecies an entity of a qualitative model, which carries a level instead of an amount
Transition what the level of a qualitative species becomes, and under which condition
Input a qualitative species a transition reads, with the sign of its influence
Output a qualitative species a transition changes, with the effect it has on it
FunctionTerm one row of the transition table: a condition and the level it results in
DefaultTerm the level of a transition in every state no function term covers
Distributions (distrib)