ModelReuse

Altering existing models

For the case of (cardiac) electrophysiology models, there are generally two modifications that you might wish to make to existing models:

1. the addition of a new current; and
2. a new scale factor for an existing current.

Assume the model encapsulation structure:

model
  Na_1
  Na_2
  K_1
  K_2
  Ca_1
  Ca_2
  Ca_3
  membrane
  ionDynamics

with the Ca, Na, and K current values being available via the model component and the membrane potential equation dV/dt = Itotal/Cm and ionDynamics defining equations like dion/dt = ion_flux with ion flux defined by some equation involving the total current for each ionic specie.

To add a new current to this hierarchy would involve importing all the existing top level components (under model), adding in the new current definition, rebuilding the encapsulation hierarchy and connections, and updating ionDynamics to include the new current as appropriate.

An alternative is to define (within the original model) additional ion specific currents which come into the top level model component (as parameter values) and are incorporated into the membrane potential and ion dynamics equations. By doing this, model authors are free to import the top level model component, define their new current(s) and connect it to the appropriate ion specific additional current. This is also a good way to define a (potassium) stimulus current without the need to defining a special stimulus current variable within the model.

This takes care of case (1) above, but initially doesn't seem to help with case (2). For case (2), you typically might be wanting to add a new dependence to an existing current. For example, you want to add a Hill-type relationship defining the effect of [ATP]i on the maximal relative conductivity of a particular channel. The trick is to add this scale factor to the original current equation without having to import a bunch of components and redefining connections and equations within those existing models.

One potential solution would be to use the additional current mechanism from above. You import the model component, which gives you access to the current values. You can then calculate the actual current value you want for the particular case (i.e., ICa_1s = ICa_1 * sf) and then subtract the original current and add the scaled current to the additional current (i.e., ICa_additional = ICa_1s - ICa_1). I (andre) have just started looking at this approach, but it looks like it might work... However, this approach will not work if a particular current is used in some other way within the original model. (preliminary results suggest this approach at least works fine)