Specifying the parameters that are to be optimized

Let's review the parameters that we want the MRF to adjust.
Parameter Description
Ra cytoplasmic resistivity
cm specific membrane capacitance
g_pas specific membrane conductance everywhere except apical dendrites
A0 minimum value of the sigmoidal function of distance that governs specific membrane conductance in the apical dendrites
A A + A0 is the maximum value of the sigmoidal function
d distance at which specific conductance in the apical dendrites is halfway between A0 and A + A0

But we're not going to have the MRF access these directly. Instead, we want to tell the MRF to control the surrogate variables Ra_, cm_, g_pas_, A0_, A_, and d_.

  1. Click on the MRF's Parameters / Add Parameter
    This brings up a variable name browser (where have we seen that before?).
  2. Click in the edit field of the variable name browser, type Ra_, then click on the Accept button.
  3. Do the same for cm_, g_pas_, A0_, A_, and d_.

The surrogate variables will appear in the left panel of the MRF.

Save the MRF to a session file!

Viewing (and changing) parameter values

Click on the MRF's
  Parameters / Parameter Panel

Change cm_ and see what happens. In the Parameter panel, increase cm_ to 2, then click on Error Value in the iclamp soma Generator. To restore cm_ back to its original value, click on the checkbox to the right of the cm_ button.

The checkboxes to the left of the parameter buttons specify which parameters the MRF is allowed to adjust. A check mark means the MRF can alter that parameter's value.


At this point we have set up the iclamp soma Generator, which emulates protocol 1, and told the MRF what parameters to optimize.

The next step is to try optimizing the model with this Generator.


[ Outline | Previous | Next ]


NEURON hands-on course
Copyright © 1998-2012 by N.T. Carnevale and M.L. Hines, all rights reserved.