SBML type "Model"

Description

The central SBML element. Contains the Species, Reactions, Compartments and other components of the model. See the SBML specification, at the reference, for further details.

Instantiation

Objects can be created by calls of the form new("Model", ...).

Slots

id:

Object of class "character" uniquely identifying this component.

name:

Object of class "character" naming this component.

functionDefinitions:

Object of class "list" containing FunctionDefinitions. The names of the list correspond to the IDs of the elements.

unitDefinitions:

Object of class "list" containing UnitDefinitions. The names of the list correspond to the IDs of the elements.

compartments:

Object of class "list" containing Compartments. The names of the list correspond to the IDs of the elements.

species:

Object of class "list" containing Speciess. The names of the list correspond to the IDs of the elements.

parameters:

Object of class "list" containing Parameters. The names of the list correspond to the IDs of the elements.

rules:

Object of class "list" containing Rules.

reactions:

Object of class "list" containing Reactions. The names of the list correspond to the IDs of the elements.

events:

Object of class "list" containing Events. The names of the list correspond to the IDs of the elements.

layouts:

Object of class "list" containing Layouts. The names of the list correspond to the IDs of the elements.

speciesTypes:

Object of class "list" containing SpeciesTypes. The names of the list correspond to the IDs of the elements.

compartmentTypes:

Object of class "list" containing CompartmentTypes. The names of the list correspond to the IDs of the elements.

constraints:

Object of class "list" containing Constraints. The names of the list correspond to the IDs of the elements.

initialAssignments:

Object of class "list" containing InitialAssignments.

modelHistory:

Object of class ModelHistory recording the history of the model.

metaId:

Object of class "character" that is an XML ID "described" by an RDF resource. This links an SBML element to an RDF resource. RDF may appear anywhere in an SBML element, but is usually placed inside the annotation element.

notes:

Object of class "character" containing user-readable XHTML notes about an element.

annotation:

Object of class "character" containing additional machine-readable information about an element, usually as RDF, such as BioPAX. This is where application-specific data belongs.

cvTerms:

Object of class "list" containing instances of CVTerm associated with this element.

sboTerm:

Object of class "integer" identifying a term in the Systems Biology Ontology (SBO).

Extends

Class "SBase", directly.

Methods

id

signature(object = "Model"): gets the id slot

id<-

signature(object = "Model"): sets the id slot

name

signature(object = "Model"): gets the name slot

name<-

signature(object = "Model"): sets the name slot

compartments

signature(object = "Model"): gets the compartments slot

compartments<-

signature(object = "Model"): sets the compartments slot

events

signature(object = "Model"): gets the events slot

events<-

signature(object = "Model"): sets the events slot

functionDefinitions

signature(object = "Model"): gets the functionDefinitions slot

functionDefinitions<-

signature(object = "Model"): sets the functionDefinitions slot

layouts

signature(object = "Model"): gets the layouts slot

layouts<-

signature(object = "Model"): sets the layouts slot

parameters

signature(object = "Model"): gets the parameters slot

parameters<-

signature(object = "Model"): sets the parameters slot

species

signature(object = "Model"): gets the species slot

species<-

signature(object = "Model"): sets the species slot

reactions

signature(object = "Model"): gets the reactions slot

reactions<-

signature(object = "Model"): sets the reactions slot

rules

signature(object = "Model"): gets the rules slot

rules<-

signature(object = "Model"): sets the rules slot

unitDefinitions

signature(object = "Model"): gets the unitDefinitions slot

unitDefinitions<-

signature(object = "Model"): sets the unitDefinitions slot

compartmentTypes

signature(object = "Model"): gets the compartmentTypes slot

compartmentTypes<-

signature(object = "Model"): sets the compartmentTypes slot

constraints

signature(object = "Model"): gets the constraints slot

constraints<-

signature(object = "Model"): sets the constraints slot

initialAssignments

signature(object = "Model"): gets the initialAssignments slot

initialAssignments<-

signature(object = "Model"): sets the initialAssignments slot

speciesTypes

signature(object = "Model"): gets the speciesTypes slot

speciesTypes<-

signature(object = "Model"): sets the speciesTypesslot

modelHistory

signature(object = "Model"): gets the modelHistory slot

modelHistory<-

signature(object = "Model"): sets the modelHistory slot

stoichiometryMatrix

signature(object = "Model"): calculates the stoichiometry matrix of the model

Author(s)

Michael Lawrence

References

http://sbml.org/documents/

Results