Le in PMC 207 June 02.Hucka et al.Pagemathematical interpretation. Simulators and
Le in PMC 207 June 02.Hucka et al.Pagemathematical interpretation. Simulators and other numerical analysis software may possibly ignore CompartmentType objects and references to them in a model. There’s no mechanism in SBML for representing hierarchies of compartment varieties. 1 CompartmentType object instance can not be the subtype of another CompartmentType object; SBML offers no implies of defining such relationships. 4.five. The id and name attributesAs with other major class of objects in SBML, CompartmentType includes a mandatory attribute, id, utilised to provide the compartment kind an identifier. The DEL-22379 identifier should be a text string conforming for the syntax permitted by the SId information variety described in Section 3..7. CompartmentType also has an optional name attribute, of type string. The name and id attributes must be utilized as described in Section 3.three. 4.5.two The sboTerm attributeCompartmentType inherits an optional sboTerm attribute of type SBOTerm from its parent class SBase (see Sections 3..9 and 5). When a value is given to this attribute in a CompartmentType instance, the worth should be an SBO identifier referring to a material entity (i.e terms derived from SBO:0000240, “material entity”). The connection is on the form “the compartment type is actually a X”, where X is the SBO term. The term chosen must be probably the most precise (narrow) 1 that captures the role of the compartment sort inside the model. four.5.three ExamplesThe following partial SBML example illustrates a compartment form utilized to relate with each other numerous individual compartments in a hypothetical model.Author Manuscript Author Manuscript Author Manuscript Author Manuscript4.6 Species kinds The term species form refers to reacting entities independent of place. These include things like very simple ions (e.g protons, calcium), uncomplicated molecules (e.g glucose, ATP), significant molecules (e.g RNA, polysaccharides, and proteins), and other people. The SpeciesType object class is intended to represent these entities. Its definition is shown in Figure 4. SpeciesType objects are incorporated in SBML to allow Species (Section four.8) of the very same form to become associated together. It’s a conceptual construct; the existence of SpeciesType objects within a model has no impact around the model’s numerical interpretation. Except for the requirement for uniqueness of speciesspecies sort combinations situated in compartments (described in Section four.8.2), simulators as well as other numerical evaluation software program may PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/23637907 ignore SpeciesType structures and references to them inside a model.J Integr Bioinform. Author manuscript; obtainable in PMC 207 June 02.Hucka et al.PageThere is no mechanism in SBML for representing hierarchies of species varieties. 1 SpeciesType object instance can not be the subtype of yet another SpeciesType; SBML provides no signifies of defining such relationships. four.6. The id and name attributesAs with other big object classes in SBML, SpeciesType features a mandatory attribute, id, employed to offer the species form an identifier. The identifier has to be a text string conforming towards the syntax permitted by the SId data type described in Section three..7. SpeciesType also has an optional name attribute, of type string. The name and id attributes should be utilised as described in Section 3.three. 4.6.two The sboTerm attributeSpeciesType inherits an optional sboTerm attribute of sort SBOTerm from its parent class SBase (see Sections three..9 and 5). When a worth is provided to this attribute in a SpeciesType instance, the worth should be an SBO identifier referring to a material entity (i.e terms derived fro.
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