We'll be analyzing a couple of models in order to answer these questions:
Moore JW, Stockbridge N, Westerfield M (1983)
On the site of impulse initiation in a neurone.
J. Physiol. 336:301-11
This one doesn't have any mod files, but there's plenty to keep us busy.
The model archive moore83.zip has already been downloaded and unzipped. You'll find its contents in course/modeldb/moore83
Go to course/modeldb/moore83 and read the README file. Does it provide any more clues?
The PointProcessManager shows a shape plot of the cell.
To see what sections exist and how they are connected, type
topology()and
forall psection()at the oc> prompt.
Was this model specified by hoc code, or was a CellBuilder used?
Exit the simulation and search the hoc files for create statements.
Under UNIX type
grep create *hocUnder MSWin you can open a Command Prompt window, cd to the course/modeldb/moore83 directory, and then type
c:\nrn54\bin\grep create *hocAlternatively you could try Windows Explorer's semi-useful Search function, or open each hoc file with a text editor and search for create.
If no hoc file contains the create keyword, maybe the CellBuilder was used.
Run mosinit.hoc again and look for a CellBuilder.
If you don't see one, maybe a Window Group Manager is hiding it.
Click on NEURON Main Menu/Window and look for one or more window names that are
missing a red check mark. If you see one, scroll down to it and release the mouse button.
If a CellBuilder pops up, examine its Topology, Subsets, Geometry, and Biophysics pages.
Do they agree with the output of forall psection()?
Now you know how the model cell was implemented. Suppose you wanted to get a copy of it that you could use in a program of your own. Would you do this by saving a CellBuilder to a new session file, or by using a text editor to copy create, connect, insert etc. statements from one of the hoc files?
Hints: look for an xpanel statement in one of the hoc files.Find the procedures that implement the actions that are caused by clicking on a button.
Read about xpanel, xbutton, and xvarlabel in the help files.
The remaining statements do one or more of the following:
change model parameters (e.g. spatial distribution of HH in the dendrite)
change stimulus parameters (e.g. stimulus location and duration)
change simulation parameters
Why does the space plot automatically save traces every 0.1 ms?
Hint: analyze the procedure that actually executes a simulation
Which hoc file contains this procedure?
What procedure actually changes the stimulus location, duration, and amplitude? Read about PointProcessManager in the help files.
Mainen ZF, Sejnowski TJ (1996)
Influence of dendritic structure on firing pattern in model neocortical neurons.
Nature 382:363-6
This one has interesting anatomy and several mod files.
The model archive patdemo.zip has already been downloaded and unzipped. Its contents are in course/modeldb/patdemo
Read the README.txt file in course/modeldb/mainen96 . Any more clues here?
This program grafts a stylized myelinated axon onto 3d specifications of detailed morphometry.
Where is the hoc code that accomplishes this grafting?
If you run mosinit.hoc and then try to import one of the cell
morphologies into the CellBuilder, do you also get the axon?
Length and diameter are scaled in order to compensate for the effect of
spines on dendritic surface area. Find the procedure that does this.
What is an alternative way to represent the effect of spines?
nseg is adjusted in each section so that no segment is longer than 50 um. What procedure does this?
Five active currents and one pump mechanism are included.
Examine these mod files.
Do they appear to be compatible with CVODE?
Check them with modlunit.
Did you find any inconsistencies?
Do any of these seem likely to affect simulation results?
Are there any other errors?
How might you fix the errors that you found?
Restart nrngui and load the CellBuilder's session file.
Assign a plausible set and spatial distribution of biophysical properties
and save to a session file.
Instrument your new model and run a simulation.
Save the model, with instrumentation, to a session file.