The stoichiometryattribute is of form 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 one of stoichiometryor stoichiometryMathshould be defined in a provided 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 applied in preference to stoichiometryMathwhen a species’ stoichiometry is really a straightforward scalar quantity (integer or decimal). When the stoichiometry is a rational quantity, or when it is a far more difficult formula, stoichiometryMathmust be utilized. The MathML expression in stoichiometryMathmay also refer to identifiers of entities within a model (except reaction identifiers), as discussed in Section three.four.3. However, the only species identifiers that may be utilized in stoichiometryMathare those referenced within the Reaction list of reactants, items and modifiers. The stoichiometryattribute along with the stoichiometryMathelement, when either is used, is each interpreted as a aspect applied towards the reaction price to give the price of alter on the species identified by the speciesattribute. This is the regular interpretation of a stoichiometry, but in SBML, a single more consideration must be taken into account. The reaction rate, which is the result from the KineticLaw mathelement, is usually inside the model’s substance per time units. Having said that, the price of modify of 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. If the units are different, the stoichiometry need to incorporate a conversion factor for converting the model’s substance units for 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 the stoichiometryattribute if stoichiometryis employed. If as an alternative stoichiometryMathis utilized, then the product of the model’s substance units instances the stoichiometryMathunits ought to match the substance units with the species. Note that in either case, in the event the species’ units and also the model’s default substance units will be the same, the stoichiometry ends up getting a dimensionless number and equivalent towards the regular chemical stoichiometry found in textbooks. Examples and more explanations of this are offered in Section 4.three.6. The following is often a very simple instance of a species reference for species ” X0″, with stoichiometry ” 2″, within a list of reactants within a reaction getting the identifier ” J”:Author Manuscript Author Manuscript Author Manuscript Author ManuscriptJ Integr Bioinform. Author manuscript; readily available in PMC 207 June 02.Hucka et al.PageAuthor Manuscript Author Manuscript Author Manuscript Author ManuscriptThe following is often a extra complex example of a species reference for species “X0”, having a stoichiometry formula consisting of a rational quantity:A species can occur far more than once inside the lists of reactants and merchandise of a given Reaction instance. The powerful stoichiometry to get a species inside a reaction would be the sum from the stoichiometry values given in the SpeciesReference GS-4997 objects inside the list of products minus the sum of stoichiometry values given within the SpeciesReference objects within the list of reactants. A optimistic value indicates the species is correctly a product and a damaging value indicates the species is effec.