Step 5. Specify biophysics

The Biophysics page is where we specify the biophysical attributes (e.g. Ra, cm, ion channels, buffers, pumps) of subsets and individual sections. Just like we did in the Geometry page, we first set up a strategy, and then review and adjust parameter values. So be sure to start with Specify Strategy ON.

Once again, remember that the specification will be executed in the same order as is shown in the list of subsets and sections. If the order isn't right, or if you need more subsets, go back to the Subsets page and make the necessary changes--and then check the Geometry and Biophysics pages to make sure that your changes didn't break anything.

A. Set up a strategy

Ra and cm are uniform in this particular model, so we select the "all" subset and then click on the Ra and cm checkboxes.

Notice that when you select a subset or section in the middle panel, the string above the column of checkboxes changes accordingly, i.e. in this case it reads "forsec all {". Also notice that the corresponding part of the shape plot turns red
(you are working along with this tutorial, aren't you?). These visual reminders can help you verify that
    (1) the subsets have been properly constructed
    (2) you're assigning properties to the right section or subset.

The apicals have the hh mechanism, so we click on apicals and then on hh.

The soma and axon also have hh, while the basilars have pas

Now we are ready to click on the Specify Strategy box to turn it OFF,

B. Execute the strategy

The middle panel of the Geometry page lists all of the sets and sections that we selected when we set up our strategy. Beneath each set or section name we also see, indented slightly, the names of the mechanisms that we are inserting. We proceed by clicking on each mechanism, and review and adjust its parameters according to the design we layed out for this model.

Right off the bat, we see that the value of Ra is not right for the "all" subset.

So we change it to the desired value.

The default value of cm is OK (1 uf/cm2 -- you did check it, right?), so we leave it alone.

For the apicals subset, we must change gnabar_hh, gkbar_hh, and el_hh from their defaults . . .

 . . . to what we need.

Notice that an x marks each mechanism with one or more parameters that have been changed from their defaults.

The soma and axon sections use the default hh values.

For the bas section, we change e_pas from its default (-70 mV) to the desired value (-65mV).

We're almost done -- but first, save this to a session file!

Next we consider how to use the model specification, and what can be done with the Management page.

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