Overview
We will use an MRF to adjust the parameters of a model
to try to get the best match to data obtained with two experimental protocols.
To this end, we must set up two Generators--one for each protocol.
For each Generator, we must specify
- a list of "protocol constants" that describe the experimental conditions
(think "independent variables")
- a list of the "observed variables" ("dependent variables")
- the experimental results
In the context of this exercise,
the protocol constants are IClamp[0].amp and IClamp[1].amp,
the observed variables are soma.v(0.5) and dendrite_1[9](0.5),
and the experimental results are the recordings of these variables.
Let's start by setting up the Generator for protocol 1.
Configure an MRF to do a "run fitness" optimzation
In the NEURON Main Menu toolbar, click on
Tools / Fitting / Multiple Run Fitter
Release the mouse button and an MRF appears.
Drag it to a convenient location on your screen.
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".
Give the Run Fitness Generator a descriptive name.
This is the Run Fitness Generator for protocol 1,
in which current is injected into the soma, so
change its name to "iclamp soma".
- Click on
Generators / Change Name
"Change" should appear to right of the Generators button.
- In the MRF's right panel, double click on "Unnamed single run protocol"
- Type "iclamp" in the dialog box's edit field, then click its Accept button.
The right panel of the MRF will show the Generator's new name.
We need to see this Generator.
We have to see the Generator
before we can get our experimental data into it.
- Click on Generators / Display
Now "Display" appears to the right of the Generators button.
- Double click on "iclamp soma", and up pops up a tiny window titled "MulRunFitter[0] Generators".
- Tell it the name of the dependent variable.
Click on the iclamp soma Generator's Fitness button,
and select the item "Variable to fit" from the popup menu.
This brings up a "variable name browser"
that looks and works just like a graph's "Plot what?" tool.
- Click inside the edit field of the variable name browser and type
soma.v(0.5)
Then click on its Accept button.
The variable name browser will go away,
but our Generator looks unchanged.
We need to make the MRF redraw it.
But first, save the MRF to a session file!
I called mine mrf.ses
Redrawing the iclamp soma Generator
Click on the iclamp soma Generator's "Close" button
(NOT the MRF's Close button!).
To see the Generator again, make sure the MRF is in "Display" mode,
then click on "iclamp soma" in its right panel.
If you made a mistake and clicked on the MRF's Close button,
both the MRF and the iclamp soma Generator went away.
But since you saved the MRF to a session file, it's easy to restore--just
xopen mrf.ses
Here's what the redrawn Generator looks like.
Notice that the blue area above the graph has three rows.
The top row shows the name of the protocol on the left.
The middle row shows the name of the variable to fit on the right.
Next to do: load data into this Generator.
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NEURON hands-on course
Copyright © 1998-2012 by N.T. Carnevale and M.L. Hines,
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