Using the CellBuilder
Physical System
A mammalian CNS neuron
Conceptual Model
Ball-and-stick approximation to cell
Simulation
Computational implementation of the conceptual model
This will be constructed with the CellBuilder,
a graphical tool for building and managing models of individual cells.
With this and other GUI tools, you will
- set up a "virtual experimental preparation" (the model cell itself).
- set up a "virtual lab rig".
- Simulation control: RunControl
- Instrumentation:
Stimulator--PointProcessManager configured as IClamp
Graphs--v vs. t, v vs. distance ("space plot")
You will also learn a simple but effective strategy for
modular organization of your programs.
- Separate the specification of the representation of the
biological system (anatomy, biophysics, connections between
cells in a network . . . )
from other items, such as the specification of instrumentation
(voltage or current clamps, graphs etc.) and controls
(e.g. RunControl panel).
- Use a short program that pulls all of the pieces together.
Modular organization makes it easier to
- develop and debug models
- reuse the same model cell in many different kinds of simulation experiments
- perform the same kind of experiment on many different model cells
Getting started
Get to a working directory where you have permission to write files.
Suggestion: start NEURON with exercises/cellbuilder as the working directory.
Hints
UNIX/Linux: cd to the exercises/cellbuilder
directory,
and enter the command line
nrngui
MSWin: double-click the nrngui icon on the desktop.
Look at NEURONMainMenu / File / recent dir.
If exercises/cellbuilder
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
- To start a CellBuilder, click on
NEURONMainMenu / Build / CellBuilder.
- CellBuilder overview and hints.
- 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 exercises/cellbuilder 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 & 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
- Here are sample init.hoc and
initial rig.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 an "evolutionary sequence"
of models that differ only in certain key points.
- 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 © 1998-2012 by N.T. Carnevale and M.L. Hines,
all rights reserved.