Ball - Stick model

Physical System

Model

Ball-Stick approximation to cell

Simulation

The computational implementation of the conceptual model will use the CellBuilder, a graphical tool for building and managing models of individual cells. In overview, you will
  1. set up a "virtual experimental preparation" (the model cell itself).
  2. set up a "virtual lab rig".

You will also learn a simple but effective strategy for modular organization of your programs.

Modular organization makes it easier to

Getting started

Get to a working directory where you have permission to write files.
Suggestion: start NEURON with course/ballstk as the working directory.
Hints
UNIX/Linux: cd to the course/init directory, and enter the command line
    nrngui

MSWin: double-click the nrngui icon on the desktop. Look at NEURONMainMenu / File / recent dir. If course/ballstk appears in the menu list, select it. Otherwise, use NEURONMainMenu / File / working dir to bring up a directory browser that you can use to navigate to the desired location.

Making the representation of the biological properties

Use the CellBuilder to make a simple ball and stick model that has these properties:

Section Anatomy Compartmentalization Biophysics
soma length 20 microns
diameter 20 microns
nseg = 1 Ra = 160 ohm cm, Cm = 1 uf/cm2
Hodgkin-Huxley channels
dend length 1000 microns
diameter 5 microns
nseg = 1 Ra = 160 ohm cm, Cm = 1 uf/cm2
passive with Rm = 10,000 ohm cm2

    Hints
  1. To start a CellBuilder, click on
       NEURONMainMenu / Build / CellBuilder.
  2. CellBuilder overview and hints.
  3. Helpful items in the on-line Programmer's Reference :
    diam    L    nseg    hh    pas

Using the representation of the biological properties

At this point you should have :
1. entered the specification of the ball & stick model in the CellBuilder
2. saved the CellBuilder to a session file called ballstk.ses and verified what you saved
3. exited NEURON

In the course/ballstk directory, make an init.hoc file with the contents

	// load the GUI tools
	load_file("nrngui.hoc")
	// your specification of the model
	load_file("ballstk.ses")
	// your GUI
	load_file("rig.ses")
Make a beginning rig.ses file with the single line
	print "ready!"

Actually you could put any innocuous statements you like into the rig.ses file, because you'll eventually overwrite this file with a custom user interface that you construct.

Start NEURON with the init.hoc argument. Under UNIX use the command

	nrngui init.hoc
Under MSWindows just double click on the init.hoc file in the file manager ("Windows Explorer").

Exercises

1. Establish that the representation in the computer basically corresponds to the model.
Connectivity? (type topology())
Soma area? (type area(0.5))
Are the properties what you expect? Try
	soma psection()
	dend psection()

2. Use the NEURONMainMenu toolbar to construct an interface that allows you to inject a stimulus current at the soma and observe a plot of somatic Vm vs. time.

3. When a current stimulus is injected into the soma, does it flow into the dendrite properly? Hint: examine a space plot of membrane potential.

Saving and Retrieving the Experimental Rig

You now have a complete setup for doing simulation experiments. The CellBuilder, which specifies your "experimental preparation," is safe because you saved it to the session file ballstk.ses. However, the GUI that constitutes your nicely-configured "lab rig" (the RunControl, PointProcessManager, graph of v vs. t, and space plot windows) will be lost if you exit NEURON prematurely or if the computer crashes.

To make it easy to reconstitute the virtual lab rig, use the Print and File Window Manager (PFWM) to save these windows to a session file. Here's how to bring up the PFWM and use it to select the windows for everything but the CellBuilder, then save these windows to a session file called rig.ses. This will allow you to immediately begin with the current GUI.

Test rig.ses by using NEURONMainMenu / File / load session to retrieve it. Copies of the "lab rig" windows should overlay the originals. If so, exit NEURON and then restart it with the init.hoc argument. It should start up with the windows that you saved.

More exercises

4. How does the number of segments in the dendrite affect your simulation?
Turn on Keep Lines in the graph of Vm vs. t so you will be able to compare runs with different nseg.
Then in the interpreter window execute the command
   dend nseg *= 3
and run a new simulation. Repeat until you no longer see a significant difference between consecutive runs.
Finally, use the command
   dend print nseg
to see how many dendritic segments were required.

5. Is the time step (dt) short enough?

6. Here's something you should try on your own, perhaps after class tonight: using the CellBuilder to manage models "on the fly."

Footnotes and Asides

  1. Here are sample init.hoc and initial rig.ses files.

  2. The CellBuilder can be used to make your own "digital stem cells." If you have a model cell that you would like to return to later, save the CellBuilder to a session file. To bring the model back, just retrieve the session file. This is a good way to create an "evolutionary sequence" of models that differ only in certain key points.

  3. The CellBuilder can also be used to manage models based on detailed morphometric reconstructions. This is covered in a later exercise.


NEURON hands-on course
Copyright © 1998-2010 by N.T. Carnevale and M.L. Hines, all rights reserved.