Step 3. Configure a MultipleRunFitter to do a "run fitness" optimization

Here we create a new Multiple Run Fitter, and use it to create a Run Fitness Generator. This is very similar to what we did in the tutorial on optimizing a function.

Might as well start fresh--quit NEURON, then use NEURON to execute init_iclamprawmodel.hoc

A. Create a Multiple Run Fitter.

We saw how to do this in the first tutorial. In the NEURON Main Menu toolbar, click on
   Tools / Fitting / Multiple Run Fitter

Release the mouse button and a Multiple Run Fitter appears.
We'll call it "MRF".

B. We need a tool to perform a "run fitness" optimization.

Create a Run Fitness Generator by clicking on the MRF's
   Generators / Add Fitness Generator / Add Run Fitness

Release the mouse button, and the right panel of the MRF shows an item called "Unnamed single run protocol".

C. Give the Run Fitness Generator a descriptive name.

We're going to use this Run Fitness Generator to calculate the difference between our experimental data and simulated current clamp experiments that use the model we created. To remind ourselves of its purpose, we change its name from "Unnamed single run protocol" to "iclamp".

We saw how to do this in the first tutorial.

  1. Switch the MRF to "change name" mode by clicking on
       Generators / Change Name
    "Change" should appear to right of the Generators button.
  2. In the MRF's right panel, double click on "Unnamed single run protocol"
  3. Enter the string "iclamp" into the dialog box's edit field, then click its Accept button.

The right panel of the MRF shows the new name.

D. We need to see this Run Fitness Generator.

We need to get our experimental data into our "iclamp" Run Fitness Generator. To do that, we have to see the Generator.

  1. Click on the MRF's Generators / Display to put it in "display" mode.
    Now "Display" appears to the right of the Generators button.
  2. Double click on "iclamp", and up pops up a tiny window titled "MulRunFitter[0] Generators".

    From now on we'll call this the iclamp Run Fitness Generator.

  3. We have to tell our iclamp Run Fitness Generator which variable in our model it needs to test. Click on this thing's Fitness button, and select the item "Variable to fit" from the popup menu.

    This brings up a "variable name browser"

    An aside: this looks and works just like the tool we have used elsewhere to add variables to a Graph's plot list (remember "Plot what?").

  4. Click inside the edit field of the variable name browser tool and type
       soma.v(0.5)
    as shown here

    Then click on its Accept button.

The variable name browser will go away, but our iclamp Run Fitness Generator looks unchanged. We need to make the MRF redraw it.

But first, save the MRF to a session file! Call it iclampfit.ses

Redrawing the iclamp Run Fitness Generator

Click on the iclamp Run Fitness Generator's "Close" button. We get it back by making sure the MRF is in "Display" mode, and then clicking on "iclamp" in its right panel.

If you made a mistake and clicked on the MRF's Close button, both the MRF and the iclamp Run Fitness Generator went away. But since you saved the MRF to a session file, it's easy to restore.
Here's what the redrawn Run Fitness Generator looks like.

Next we will load our data into this Run Fitness Generator.

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Copyright © 2004-2009 by N.T. Carnevale and M.L. Hines, All Rights Reserved.