The stoichiometryattribute is of kind double. The stoichiometryMathelement is implemented as
The stoichiometryattribute is of type 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 offered 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 really should be employed in preference to stoichiometryMathwhen a species’ stoichiometry can be a uncomplicated scalar quantity (integer or decimal). When the stoichiometry is usually a rational number, or when it’s a far more difficult formula, stoichiometryMathmust be made use of. The MathML expression in stoichiometryMathmay also refer to identifiers of entities in a model (except reaction identifiers), as discussed in Section three.four.three. Nonetheless, the only species identifiers that may be made use of in stoichiometryMathare those referenced inside the Reaction list of reactants, items and modifiers. The stoichiometryattribute as well as the stoichiometryMathelement, when either is employed, is every interpreted as a aspect applied to the reaction rate to give the price of alter of the species identified by the speciesattribute. This really is the regular interpretation of a stoichiometry, but in SBML, 1 extra consideration must be taken into account. The reaction rate, which can be the outcome on the KineticLaw mathelement, is usually inside the model’s substance per time units. Even so, the rate of adjust with the species will involve the species’ substance units (i.e the units identified by the Species object’s substanceUnitsattribute), and these units could be distinct from the model’s default substance units. In the event the units are distinct, the stoichiometry should really incorporate a conversion factor for converting the model’s substance units towards the species’ substance units. The conversion factor is PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/26346521 assumed to be included in the scalar worth in the stoichiometryattribute if stoichiometryis employed. If rather stoichiometryMathis applied, then the item of the model’s substance units R-1487 Hydrochloride occasions the stoichiometryMathunits should really match the substance units of the species. Note that in either case, in the event the species’ units and also the model’s default substance units are the identical, the stoichiometry ends up getting a dimensionless quantity and equivalent to the regular chemical stoichiometry discovered in textbooks. Examples and much more explanations of this are given in Section 4.three.6. The following is a very simple instance of a species reference for species ” X0″, with stoichiometry ” 2″, within a list of reactants inside a reaction possessing 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 can be a a lot more complicated example of a species reference for species “X0”, having a stoichiometry formula consisting of a rational number:A species can happen additional than after within the lists of reactants and products of a offered Reaction instance. The efficient stoichiometry for any species inside a reaction would be the sum of the stoichiometry values offered within the SpeciesReference objects inside the list of products minus the sum of stoichiometry values offered inside the SpeciesReference objects within the list of reactants. A good worth indicates the species is successfully a product and also a unfavorable worth indicates the species is effec.
