In a description of the SBML standard, namely Hucka et al., The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core, J Integr Bioinform. ; 12(2): 266. doi:10.2390/biecoll-jib-2015-266, a point of the specification is stated: "4.11.2 SimpleSpeciesReference As mentioned above, every species that enters into a given reaction must appear in that reaction’s lists of reactants, products and/or modifiers. " One maddening element of this is that a species can apparently be all three things! A self growth of A to increase the amount A, self-catalyzed by A. Does anyone know if appearance of a species in one list is sufficient, or (for example) if I have a mass action expression of compound A, does A have to be in both the reactants AND the modifer list? More to the point: As far as I can tell, sbmlexport does not export modifers. They're just not there. So if one has reactions like A->B, but the reaction rate expresssion is r=k*A*C, where C is a species, then sbml isn't conformal. Am I missing something? Improperly using sbmlexport? If modifiers are NOT there, will modifers be included in a future release? Right now I have a python script that captures all of the species in reactions that are not reactants or products, but it would be nice to have. This brings up a question. Suppose I have a function dependent upon species, but indirectly. For example, A parameter defined by a repeat assignment: Glut4 = f(Plasma.Insulin); for a reaction of Plasma.Glucose --> muscle.Glucose I have the reaction rate rp2m = k * Glut4 * Plasma.Glucose; Given those equations, is Plasma.Insulin a modifier of the reaction defined by rp2m?
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