This is the readme for NEURON code developed to reproduce Fig 2B from
Shepherd GM, Brayton RK (1979) Computer simulation of a
dendrodendritic synaptic circuit for self- and lateral-inhibition in
the olfactory bulb. Brain Res 175:377-82
There were typos in Figure 1 (Shepherd, private communication) where
the granule cell spine geometry should have been specified as 3 micron
length, 1 micron diameter head and 1 micron length and 0.2 micron
width neck dimensions. The granule cell compartments were 70 microns
in length and 1 micron in diameter.
The NEURON models cytoplasmic and membrane resistance, Ri, and Rm, as
well as the excitatory synaptic conductance pulse (a trapezoidal
pulse) were optimized to the original paper Fig 2B:
The above screenshot includes (black lines) that were the
result of using manually traced original curves:
Usage: Auto-launch from ModelDB or download, extract the archive and
compile the mod files in the mod directory by either
typing "nrnivmodl mod" (linux),
running mknrndll and cd'ing to the mod folder (mswin), or
dragging and dropping the mod folder onto the mknrndll icon (Mac OS X)
Then start with
nrngui mosinit.hoc (linux),
double clicking the mosinit.hoc file in windows explorer (mswin), or
dragging and dropping the mosinit.hoc file on the nrngui icon (Mac OS X).
Once the simulation has started you can either
1) optimize to find the Ri, Rm, and conductance pulse trapezoidal
shape that matches the paper: On the multiple run fitter window click
on Parameters -> Select Optimizer -> Praxis, and then click on the
Optimize button in the "MulRunFitter Optimize" box.
After a short time praxis will find the Ri ~ 90 and Rm ~ 1300.
2) or use a previously saved Multiple Run Fitter session to see the
result of optimizing. Close the MulRunFitter main window and select
from the NEURON main menu: File -> load session file, and then using
the popped up file picker, browse to the mrf folder and select
mrf5.ses, which contains the result of a previous optimization. Now
you can press the ErrorValue button on the newly opened MulRunFitter
window to generate a run. The graphs will be refreshed with optimized
For questions, please contact Tom.Morse at yale.edu.