Milestones in the modeling process

Everyone agrees on the units of time, the units of quantity, and the basis of the model

What is the "basis" of a model? This is a fairly intuitive concept, but it is often left implicit. Some modelers think of it as normalization. The basis of a molecular cell biology model might be one cell or it might be a million cells. The basis of a model of whole-animal metabolism might be a kg of body weight. The basis you choose is a matter of convenience and personal preference; it scales all your model's states and fluxes so that they can be compared to results in other laboratories. The ProcessDB team likes to use one cell as the basis for models in molecular cell biology. This means that model state variables will have units of molecules per cell or attomoles/cell. You could just as well choose a million cells as your basis, and then your state variables might have units of pmol/million cells. If we are building models of human metabolism we usually choose umol/kgBW as our units for state variables, but the choice is always yours to make! We are simply recommending that you make that choice explicit.