The stoichiometryattribute is of sort double. The stoichiometryMathelement is implemented as
The stoichiometryattribute is of form double. The stoichiometryMathelement is implemented as an element containing a MathML expression. These two are mutually exclusive; only a single of stoichiometryor stoichiometryMathshould be defined inside a given SpeciesReference instance. When neither the attribute nor the element is present, the value of stoichiometryin the SpeciesReference instance defaults to ” “. For maximum interoperability, SpeciesReference’s stoichiometryattribute must be used in preference to stoichiometryMathwhen a species’ stoichiometry is a straightforward scalar number (integer or GSK2269557 (free base) decimal). When the stoichiometry is a rational number, or when it can be a additional complicated formula, stoichiometryMathmust be employed. The MathML expression in stoichiometryMathmay also refer to identifiers of entities within a model (except reaction identifiers), as discussed in Section 3.four.3. On the other hand, the only species identifiers that can be utilised in stoichiometryMathare those referenced in the Reaction list of reactants, products and modifiers. The stoichiometryattribute as well as the stoichiometryMathelement, when either is used, is each and every interpreted as a aspect applied towards the reaction price to provide the price of change in the species identified by the speciesattribute. This really is the typical interpretation of a stoichiometry, but in SBML, a single additional consideration has to be taken into account. The reaction price, that is the result in the KineticLaw mathelement, is generally inside the model’s substance per time units. On the other hand, the rate of alter from the species will involve the species’ substance units (i.e the units identified by the Species object’s substanceUnitsattribute), and these units might be various from the model’s default substance units. If the units are various, the stoichiometry need to incorporate a conversion factor for converting the model’s substance units to the species’ substance units. The conversion aspect is PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/26346521 assumed to be included in the scalar worth from the stoichiometryattribute if stoichiometryis applied. If as an alternative stoichiometryMathis employed, then the product on the model’s substance units occasions the stoichiometryMathunits ought to match the substance units in the species. Note that in either case, when the species’ units and also the model’s default substance units are the same, the stoichiometry ends up being a dimensionless quantity and equivalent for the standard chemical stoichiometry identified in textbooks. Examples and much more explanations of this are offered in Section four.3.six. The following is actually a easy example of a species reference for species ” X0″, with stoichiometry ” 2″, inside a list of reactants within a reaction obtaining the identifier ” J”:Author Manuscript Author Manuscript Author Manuscript Author ManuscriptJ Integr Bioinform. Author manuscript; offered in PMC 207 June 02.Hucka et al.PageAuthor Manuscript Author Manuscript Author Manuscript Author ManuscriptThe following is often a extra complicated example of a species reference for species “X0”, having a stoichiometry formula consisting of a rational number:A species can take place extra than once within the lists of reactants and products of a provided Reaction instance. The helpful stoichiometry to get a species within a reaction is the sum from the stoichiometry values given within the SpeciesReference objects within the list of items minus the sum of stoichiometry values offered within the SpeciesReference objects within the list of reactants. A positive value indicates the species is correctly a item along with a unfavorable worth indicates the species is effec.