SR and CR net: HFOs in Hippocampus Model README file
=====================================================
This model creates the 100-cell hippocampal model in:
Stacey WC, Lazarewicz MT, and Litt B. Synaptic Noise and Physiological
Coupling Generate High Frequency Oscillations in a Hippocampal
Computational Model. Journal of neurophysiology 102: 2342-2357, 2009.
To run the simulation
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1. Should be run in the normal (serial) installation of NEURON 6.1 or
above. Most of the code is actually written for parallel
implementation, but several functions were added that are not able to
run in parallel.
2. Unpack the zip file, keeping the file structure intact (see below)
3. Compile the nrnmech file within the \mod directory according to
your system's requirements. Move the nrnmech file to the root
directory.
4. Run netrun.hoc.
5. Currently the network creates the three files demonstrated in
Fig. 5A. Other specific parameters to simulate different conditions
need to be set as follows :
within netrun.hoc
Tstop length of simulation in ms
pyrthr the threshold to which the random
number (0-100) is compared. rnd >
pyrthr will create a noise event
basketthr same as above for synapses to basket
cells
gapstyle whenever you alter the files in
\parameters, change this number and
record what the changes were
sigfreq frequency of periodic signal. Will
have to be placed with
pr.signalSynapse(Tstop, 0, sigfreq,
cell#that_receives_stim). Cells
0-80 are the pyramidal cells
within \parameters\conn.dat
this file lists all synaptic and gap junctional
connections, based on the parameters of synapses.par
the current conn.dat has the full feedback network of
pyr - basket - pyr connections described. It also has
gap junctions between the basket cells (but these are
currently "turned off" because the conductance is 0 in
synapses.par) there are several additional conn.dat
files in the attached folder. These simply need to be
moved to the \parameters directory and renamed
"conn.dat"
\parameters\synapses.par
Here the gmax of the synapses is changed. For Figure
5B, the "5.5" in the "Bask, Pyr" line was changed to
various levels. NOTE: that due to scaling, this gmax
is divided by 20 in the network, thus "5.5" is
actually 0.275 nS I did not change the amplitude of
any other "synapses" (noise was altered by rate of
firing, not amplitude) The gap junctions at the end
have altered gmax in the same fashion. In this case
there is no scaling, and the gmax's indicated are what
are reported.
FILE EXPLANATIONS
=================
Program run in the root directory, and calls files in several branched
directories as listed below. The program is run from a batch file
that saves several parameters into the file names
Note that the program was originally written in parallel format, and
is based on legacy code written by Maciej Lazarewicz that was some of
the first parallel code used in NEURON, before the parallel version
was out of alpha. There have been many modifications since then, some
of which do not work in parallel. It is for this reason that the gap
junctions were done with the parallel format directly in the TGnet.tem
rather than the pointer method.
Unfortunately, the parallel idiom, which is slightly different even
than the current standard parallel idiom, can make this code difficult
to follow. Because of several reasons, this code is not ready for
parallel implementation. However, it is an excellent candidate for
the "bulletin board" style parallel that is currently being developed.
root folders:
\templates
****TGnet.tem //main program to build the network and
generate stimuli and noise
****PYRkop.tem //template for the pyramidal cells
****Bwb.tem //template for basket cells
Ok.tem // Okn cells not used
several others //not used
\mod
has all the channels, synapses, and gap(not used) .mod
files
\parameters
// this folder is where the connectivity and
conductance values are changed for different runs has
.dat and .par files that contain the parameters that
will be read in These files must be manually altered
to change the parameters. I used the parameter
"gapstyle" in the netrun.hoc to indicate which
parameter set I had used for gmax's (had to keep track
of this separately" also have .tem files for cells and
synapses
\library
//not used
\data
// all data saved here. Each run creates a different
filename to be saved
The main folder has the .hoc executable (there are many different
versions, all variations of below)
*****netrun.hoc //main .hoc file
loads in /templates/TGnet.tem
sets many flags and parameters
DoRun() is the main executable
pr = new TGnet() //from template folder which
contains all functions in TGnet.tem,
as well as having .pnm. class
pr.pnm.want_all_spikes()
pr.activeSynapsesRandom(.....) generates
random synaptic events in all the
cells
pr.signalSynapse(....) adds a periodic input
to a specific pyramidal cell
pr.pnm.psolve(Tstop)
pr.pnm.gatherspikes()
writes files per flags
pr.pnm.pc.gid_clear()
I make runs of files by changing parameters then
calling DoRun(), over and over
Note that, although written in pnm.pc format, I have never compiled
NEURON that way--I've just run it in basic serial format.
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