The stoichiometryattribute is of type double. The stoichiometryMathelement is implemented as
The stoichiometryattribute is of sort double. The stoichiometryMathelement is implemented as an element containing a MathML expression. These two are mutually exclusive; only 1 of stoichiometryor stoichiometryMathshould be defined inside a offered SpeciesReference instance. When neither the attribute nor the element is present, the worth of stoichiometryin the SpeciesReference instance defaults to ” “. For maximum interoperability, SpeciesReference’s stoichiometryattribute really should be used in preference to stoichiometryMathwhen a species’ stoichiometry is a straightforward scalar quantity (integer or decimal). When the stoichiometry is often a rational number, or when it can be a a lot more complex formula, stoichiometryMathmust be utilized. The MathML expression in stoichiometryMathmay also refer to identifiers of entities inside a model (except reaction identifiers), as discussed in Section three.four.three. Nonetheless, the only species identifiers that can be utilized in stoichiometryMathare those referenced in the Reaction list of reactants, products and modifiers. The stoichiometryattribute plus the stoichiometryMathelement, when either is used, is each and every interpreted as a factor applied for the reaction rate to give the rate of change on the species identified by the speciesattribute. This is the standard interpretation of a stoichiometry, but in SBML, 1 extra consideration has to be taken into account. The reaction price, that is the result in the KineticLaw mathelement, is constantly in the model’s substance per time units. Nevertheless, the rate of transform from the species will involve the species’ substance units (i.e the units identified by the Species object’s substanceUnitsattribute), and these units may well be different from the model’s default substance units. In the event the units are various, the stoichiometry should really incorporate a conversion factor for converting the model’s substance units towards the species’ substance units. The conversion aspect is PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/26346521 assumed to be included within the scalar value of your stoichiometryattribute if stoichiometryis utilized. If alternatively stoichiometryMathis made use of, then the solution of the model’s substance units times the stoichiometryMathunits must match the substance units with the species. Note that in either case, in the event the species’ units and the model’s default substance units are the same, the stoichiometry ends up getting a dimensionless quantity and equivalent towards the common chemical stoichiometry found in textbooks. Examples and much more explanations of this are provided in Section 4.three.six. The following can be a basic example of a species reference for species ” X0″, with stoichiometry ” 2″, in a list of reactants within a reaction obtaining the identifier ” J”:Author Manuscript Author Manuscript Author Manuscript Author ManuscriptJ Integr Bioinform. Author manuscript; accessible in PMC 207 June 02.Hucka et al.PageAuthor Manuscript Author Manuscript Author Manuscript Author ManuscriptThe following is really a a lot more complicated instance of a species reference for species “X0”, having a stoichiometry formula consisting of a rational quantity:A species can occur more than after within the lists of reactants and items of a provided Reaction instance. The successful stoichiometry to get a species within a reaction is definitely the sum in the stoichiometry A-1155463 site values offered within the SpeciesReference objects in the list of merchandise minus the sum of stoichiometry values given in the SpeciesReference objects within the list of reactants. A positive worth indicates the species is successfully a item in addition to a unfavorable worth indicates the species is effec.