Package org.jscience.ml.sbml

Interface Summary
MathElement This code is licensed under the DARPA BioCOMP Open Source License.
 

Class Summary
AlgebraicRule A rule that expresses equations with left-hand side of zero.
Annotations Stores the annotation metadata for an SBML node.
AssignmentRule A rule that expresses equations which set the value of variables.
Compartment A bounded container in which species are located.
Event An instantaneous discontinuous change in the state of the model when a criterion is met.
EventAssignment The variable assignments made when an Event is executed.
FunctionDefinition An association between an identifier and a mathematical function.
KineticLaw The mathematics of the rate of the enclosing Reaction.
Model This class defines a grouping of components - MathDefinitions, Compartments, Species, Reactions, Parameters, Events, Rules, and UnitDefinitions.
ModifierSpeciesReference This class defines a modifier that takes part in a Reaction.
Notes Stores the note metadata for an SBML node.
Parameter This class declares a variable for use in MathML structures.
RateRule A rule that expresses equations which set the rate of change of variables.
Reaction This class represents a reaction, which is some transformation, transport or binding process that can change the amount of one or more Species.
Rule Rules put constraints on variables in cases for which the constraint cannot be expressed as a reacion or initial value.
SBase The base class for the main SBML Level 2 data types.
SBaseId Name and id for an sbml node.
SBMLLevel2Document This class represents a SBML Level 2 Document This code is licensed under the DARPA BioCOMP Open Source License.
SBMLLevel2Reader Reads a SBML Level 2 file into a Model.
Species This class represents an entity that takes part in Reactions.
SpeciesReference A class defining a reference to a Species for use in a Reaction.
StoichiometryMath This code is licensed under the DARPA BioCOMP Open Source License.
Unit Units of measurement for quantities in an SBML model.
UnitDefinition A combination of Units to create a user-defined unit of measurement.
UnitManager Manages a collection of unit definitions.