Hi Rainer. Thanks for joining in this discussion. Your point is well taken and both Nicolas and Stefan have made the same point in different ways. I agree that if you have the kinetic laws for the reactions, you do not need the ListOfModifiers to write the ODEs, whereas you DO need the ListOfReactants and the ListOfProducts. In this situation, one could argue that the ListOfModifiers is completely unnecessary.
You pose the important question as to what uses the ListOfModifiers has in the larger world of SBML models. So far in this thread only the ability to create accurate diagrams has been highlighted, and while I think this is important it's apparently not as compelling as the need to write correct ODEs.
But I think the ListOfModifiers much more. I think it is a vital communication link between the SBML community and the experimental biology community. If SBML has only the narrow parochial goal of exchanging models among investigators who have the training and experience to understand the mathematics of biological models, then clearly the ListOfModifiers is not even necessary. I would still argue that if it is present it should be complete, but I would have no grounds for arguing that it is essential.
If, however, we have a larger goal for SBML, one in which it serves as an interface between qualitative diagrams and quantitative models, then I think the ListOfModifiers is every bit as important as the ListOfReactants and the ListOfProducts.
To me there is an important reason that the SBML specification says the kinetic law is OPTIONAL and the ListOfModifiers is REQUIRED. That reason is that the vast majority of published models have no mathematics at all. They are published as paragraphs or diagrams characterized by all the required elements of an SBML model: SpeciesTypes, Compartments, Species, and Reactions with Reactants, Products, and Modifiers. We need to be able to exchange these qualitative models just as effectively as we exchange mathematical models.
Maybe I misread the goals of the SBML community, but I think SBML can be at the forefront of a new biology. This is just my own perspective, but I've never been satisfied with systems biology or computational cell biology as isolated disciplines with their own journals, their own meetings and little or no interaction with our compatriots in the experimental biology community. I think systems biology is the only set of tools that has a chance of comprehending biological complexity, but I also think that without the insight of investigators who have spent their professional lives at the bench or in the clinic, systems biology cannot succeed any better than experimental biology can succeed without our insight.
To me, the beauty of SBML is that it opens the door to fruitful cooperation between these two essential threads of scientific thought. It does so, in large measure, because it supports the exchange of models/hypotheses that have ONLY SpeciesTypes, Compartments, Species, and Reactions with Reactants, Products, and Modifiers and still need the insight of a smart systems biologist to make them quantitative and testable.