A non-spatial ODE model contains reaction rates that specify a rate of change of species total amount in a given compartment.
In a PDE model, we have
compartment reactions: rate of change of species concentration
membrane reactions: rate of species amount crossing unit area of the membrane
The last step in importing a non-spatial model is to rescale the reactions appropriately, by clicking on “rescale reactions” in the bottom right of the window.
This opens a guided workflow that automatically rescales the image depth and the reaction rate expressions, with the goal of constructing a valid PDE model that initially reproduces the behaviour of the imported ODE model, in the following limit of the spatial model:
no initial spatial dependence of species concentrations
infinitely fast diffusion
consistent compartment volumes between ODE model and PDE model geometry