The SBML notion of a species seems peculiar, doesn it?
Well, no, or yes, depending on your definition of “peculiar”. The SBML construct called species represents a pool, that is, a set of “things” that are treated as being indistinguishable from the standpoint of the processes (reactions) in which they participate. When the “same” species (a chemical or other thing) is present in different compartments, each must be treated as a different pool. The reason for this is because the concentrations or partial pressures being different in the various compartments means that the chemical activities are different as well. Also, the pH of different compartments being different, the electrochemical properties of a given chemical entity could be different (think about an enzyme in the cytosol and a lysosome). Analytical software will therefore have to construct different state variables for the different pools, even if the pools contain the same kind of “thing”. This is actually a common concept in biochemical simulation, dating back to some of the e
