Ball - Stick model
Physical System
Model
Ball-Stick approximation to cell
Simulation
This exercise introduces the CellBuilder,
a graphical tool for building and managing models of individual cells.
After building your model cell, you will set up the instrumentation
(run control, stimulator, graphs) for exercising it.
You might think of the combination of the model cell
and the associated instrumentation as a "virtual lab rig."
You will also learn a simple but effective strategy
for managing the simulation environment that you have set up:
creating a kind of software wrapper that lets you conveniently
recreate the entire virtual lab rig.
One advantage of this approach is that it helps to separate
the specification of the model cell
from the specification of the instrumentation.
This makes it easier for you to reuse the same model cell
in many different kinds of experiments.
Making the representation
Make a simple ball and stick model with these properties:
Section |
Anatomy |
Biophysics |
soma |
length 20 microns diameter 20 microns |
Ra = 160 ohm cm, Cm = 1 uf/cm2
Hodgkin-Huxley channels |
dend |
length 1000 microns diameter 5 microns |
Ra = 160 ohm cm, Cm = 1 uf/cm2
passive with Rm = 10,000 ohm cm2 |
This is easy enough to do by programming in hoc code,
but for this exercise you should use the CellBuilder.
Overview of the CellBuilder.
Hints for using the CellBuilder.
It may be helpful to look up these terms in the
on-line Help Reference :
diam
L
nseg
hh
pas
Using the Representation
At this point you should have exported your model to ballstk.hoc
and exited NEURON.
In the course/ballstk directory, make an init.hoc file with the contents
// load the GUI tools
load_file("stdgui.hoc")
// your specification of the model
load_file("ballstk.hoc")
// your GUI
load_file("start.ses")
Make a beginning start.ses file with the single line
nrnmainmenu()
Start NEURON with the init.hoc argument.
Under unix use the command
nrniv init.hoc -
Under MSWindows, if .hoc files are associated with NEURON.EXE,
just double click on the init.hoc file in the file manager.
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 GUI to construct an interface that allows you to
inject a stimulus current at the soma and observe a plot
of somatic Vm vs. time.
Then inject a current stimulus into the soma.
Does it properly flow into the dendrite?
Saving and Retrieving the Representation
By this time you probably have a set of windows that would be very tedious to re-create.
Save your session so in the future you can immediately begin with the current GUI details
(PrintWindowManager/Session/SaveAll).
Save it with the filename start.ses.
Test it with PrintWindowManager/Session/Retrieve and open the start.ses file.
Copies of the windows should overlay the old windows.
If so, exit the program and restart it.
It should start up with the new windows.
More exercises
3) 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 issue the command
dend nseg *= 3
and run a new simulation.
Repeat until you no longer see a significant difference between consecutive runs.
Then use the command
dend print nseg
to see how many dendritic segments were required.
4) Is the time step (dt) short enough?
More about the CellBuilder
Here's a couple of things you should try on your own, perhaps after class tonight.
- Continuous Create
-- using the CellBuilder to manage models "on the fly."
This is really important!
- Examine the ballstk.hoc file
that you created with the CellBuilder.
- Export a new file (call it testfile.hoc),
but this time leave out one or more of the four categories of information
(Topology, Subsets, Geometry, Biophysics).
Compare the contents of testfile.hoc with those of ballstk.hoc
We'll use the CellBuilder's Import function later in this course.
Footnotes and Asides
- Here are sample init.hoc and
initial start.ses files.
- 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 a family of models that
differ only in certain key points.
NEURON summer course
Copyright © 1998, 1999 by N.T. Carnevale and M.L. Hines,
all rights reserved.