load_file("define_PFC.hoc") // or a hoc file that specifies the model cell's
// anatomical and biophysical properties
load_file("rigPFCmod.ses") // brings up the following:
// RunControl panel
// PointProcessManager configured as an IClamp at soma(0.5)
// Voltage axis plot of v at the current injection site
// space plot of v along at least one path that passes through the current injection site
// a Movie Run tool to generate smooth evolution of space plot over time
1. First, make sure that the load_file("custominit.hoc") statement below
has been commented out. Then double click on init.hoc or type
2. Determine the "initialization run time" INITDUR.
Use the GUI to set the IClamp's amp parameter to a value that drives
v at the current injection site to a level close to what you want.
Note how long it takes for v throughout the cell to reach steady state.
This is the value you should use for INITDUR (actually you could use
a slightly shorter time, because in the end the cell will be driven
to steady state by a voltage clamp, so it will settle a bit faster than
the simulation that uses an IClamp does).
Adjust Tstop in the RunControl panel and run another simulation
if necessary to make sure that the model is reaching steady state.
3. Exit NEURON and edit this file to make the following changes in the
assignment statements that follow these comments.
(1) Change the value assigned to INITDUR to what you determined in step 2.
(2) Change the value assigned to V0 so that it is whatever you want the
initial membrane potential at the current injection site to be.
(3) Uncomment the load_file("custominit.hoc") statement,
i.e. remove the double slashes // that precede it.
4. Restart NEURON by double clicking on init.hoc or typing
and you will see a run executed after a custom initialization.
Verify that membrane potential at the injection site is what
5. Exit NEURON and make the following additional change:
Uncomment the load_file("batchrun.hoc") command.
You will now be able to execute a family of runs by entering commands
like this at the oc> prompt:
batchrun(10, 100, -0.1, 0.02, 10)
will run 10 simulations in which the current pulse
begins at 10 ms and lasts 100 ms.
The pulse amplitudes, starting with the first run,
will be -0.1, -0.08, -0.06 . . . 0.08 nA.
Left to right, the parameters specify:
t at which each pulse starts
amplitude of the first run's current pulse
increment of pulse amplitude between runs
number of runs
INITDUR = 50 // change this according to what you discover in step 2 above
V0 = -62 // the initial v you want at the current injection site
// Uncomment the next line only after load_file("custominit.hoc") has been executed.
load_file("batchrun.hoc") // executes a family of simulations
// that step through a range of current pulses
// and shows the time course of membrane potential.