Parametric computation and persistent gamma in a cortical model (Chambers et al. 2012)

 Download zip file   Auto-launch 
Help downloading and running models
Accession:144579
Using the Traub et al (2005) model of the cortex we determined how 33 synaptic strength parameters control gamma oscillations. We used fractional factorial design to reduce the number of runs required to 4096. We found an expected multiplicative interaction between parameters.
Reference:
1 . Chambers JD, Bethwaite B, Diamond NT, Peachey T, Abramson D, Petrou S, Thomas EA (2012) Parametric computation predicts a multiplicative interaction between synaptic strength parameters that control gamma oscillations. Front Comput Neurosci 6:53 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network; Axon; Synapse; Channel/Receptor; Dendrite;
Brain Region(s)/Organism:
Cell Type(s): Neocortex L5/6 pyramidal GLU cell; Neocortex L2/3 pyramidal GLU cell; Neocortex V1 interneuron basket PV GABA cell; Neocortex fast spiking (FS) interneuron; Neocortex spiny stellate cell; Neocortex spiking regular (RS) neuron; Neocortex spiking low threshold (LTS) neuron;
Channel(s): I A; I K; I K,leak; I K,Ca; I Calcium; I_K,Na;
Gap Junctions: Gap junctions;
Receptor(s): GabaA; AMPA; NMDA;
Gene(s):
Transmitter(s): Gaba; Glutamate;
Simulation Environment: NEURON;
Model Concept(s): Oscillations; Parameter sensitivity;
Implementer(s): Thomas, Evan [evan at evan-thomas.net]; Chambers, Jordan [jordandchambers at gmail.com];
Search NeuronDB for information about:  Neocortex L5/6 pyramidal GLU cell; Neocortex L2/3 pyramidal GLU cell; Neocortex V1 interneuron basket PV GABA cell; GabaA; AMPA; NMDA; I A; I K; I K,leak; I K,Ca; I Calcium; I_K,Na; Gaba; Glutamate;
/
FRBGamma
cells
data
hoc
mod
net
README
balanal.hoc *
balcomp.hoc *
cell_templates.hoc *
des2runs.py
EFP2PSD.m
EFPgen.m
evan.hoc
finit.hoc *
fortmap.hoc *
FRBGamm.val
FRBGamma.des
gidcell.hoc *
manage_setup.hoc
singleoutput.m
spkplt.hoc *
synstrengthdef.hoc
                            
setuptime = startsw()
{xopen("hoc/defvar.hoc")}

// load balancing implies several runs.
// 0) load balancing just plain off (but will read mcomplex.dat if exists)
// 1) create a mcomplex.dat file (only one cpu needed)
// 2) create single split balance.dat file (any number of cpus can be used)
//  manually: run the balcomp program to create balance.ncpu files
// 3) run with single split load balancing on (ncpu corresponding to files from balcomp)
// add more for whole cell and multisplit load balancing
// 4) create whole cell load balance file
// 5) run with whole cell load balance file
// 6) create multisplit load balance information file
// 7) run using multisplit load balance
default_var("load_balance_phase", 0)

default_var("one_tenth_ncell", 0)
default_var("default_delay", 0.5)
default_var("ranseedbase", 1)
default_var("wholecell_prefix", "cxwhole")
default_var("multisplit_prefix", "cx")
default_var("multisplit_nhost", 256)
default_var("msoptfactor", 0.8)
default_var("nthread", 1)
default_var("savestatetest", 0)

default_var("use_gap", 1)
default_var("use_ectopic", 0)
default_var("use_inject", 1)
default_var("awake", 1)
default_var("use_traubexact", 0)
default_var("jordan_trace",1)
default_var("Figure", 0)
default_var("picrotoxin", 1)
default_var("NBQX", 1)
default_var("scale_NMDA_conductances", 1)
default_var("scale_TCR_output", 1)

default_var("jEFP1",1000)
default_var("jEFP2",2000)


default_var("spike_compress", 5)
default_var("cacheeffic", 1)  // for multisplit it is always 1
default_var("multisend", 0)
default_var("selfevents", 0)

default_var("fakerank", -1)
default_var("fakenhost", -1)
default_var("parmset",3)

default_var("Control", 0)

if (parmset==1) {
    default_var("e2e2",2)
    default_var("e2e5",2)
    default_var("e2e6",1)
    default_var("e2i2",1)
    default_var("e2i6",1)
    default_var("e4e2",1)
    default_var("e4e4",1)
    default_var("e4e5",1)
    default_var("e4e6",2)
    default_var("e4i2",1)
    default_var("e4i6",1)
    default_var("e5e2",1)
    default_var("e5e4",1)
    default_var("e5e5",1)
    default_var("e5e6",2)
    default_var("e5i2",2)
    default_var("e5i6",2)
    default_var("e6e2",1)
    default_var("e6e4",1)
    default_var("e6e5",2)
    default_var("e6e6",1)
    default_var("e6i2",2)
    default_var("e6i6",2)
    default_var("e6rt",1)
    default_var("e6tc",1)
    default_var("i2e2",1)
    default_var("i2e4",1)
    default_var("i2e5",1)
    default_var("i2e6",2)
    default_var("i2i2",2)
    default_var("i2i6",1)
    default_var("i6e4",1)
    default_var("i6e5",1)
    default_var("i6e6",2)
    default_var("i6i6",2)
    default_var("rtrt",1)
    default_var("rttc",2)
    default_var("tce2",1)
    default_var("tce4",2)
    default_var("tce5",1)
    default_var("tce6",1)
    default_var("tci2",2)
    default_var("tci6",1)
    default_var("tcrt",1)

}

if (parmset==2) {
    default_var("e2e2",2)
    default_var("e2e5",2)
    default_var("e2e6",1)
    default_var("e2i2",1)
    default_var("e2i6",1)
    default_var("e4e2",1)
    default_var("e4e4",1)
    default_var("e4e5",2)
    default_var("e4e6",1)
    default_var("e4i2",2)
    default_var("e4i6",1)
    default_var("e5e2",1)
    default_var("e5e4",1)
    default_var("e5e5",1)
    default_var("e5e6",1)
    default_var("e5i2",2)
    default_var("e5i6",2)
    default_var("e6e2",2)
    default_var("e6e4",1)
    default_var("e6e5",1)
    default_var("e6e6",1)
    default_var("e6i2",2)
    default_var("e6i6",2)
    default_var("e6rt",2)
    default_var("e6tc",2)
    default_var("i2e2",2)
    default_var("i2e4",1)
    default_var("i2e5",1)
    default_var("i2e6",1)
    default_var("i2i2",2)
    default_var("i2i6",2)
    default_var("i6e4",1)
    default_var("i6e5",2)
    default_var("i6e6",2)
    default_var("i6i6",2)
    default_var("rtrt",2)
    default_var("rttc",1)
    default_var("tce2",1)
    default_var("tce4",1)
    default_var("tce5",1)
    default_var("tce6",1)
    default_var("tci2",1)
    default_var("tci6",1)
    default_var("tcrt",1)
}

if (parmset==3) {
    default_var("e2e2",0)
    default_var("e2e5",0)
    default_var("e2e6",0)
    default_var("e2i2",0)
    default_var("e2i6",0)
    default_var("e4e2",0)
    default_var("e4e4",0)
    default_var("e4e5",0)
    default_var("e4e6",0)
    default_var("e4i2",0)
    default_var("e4i6",0)
    default_var("e5e2",0)
    default_var("e5e4",0)
    default_var("e5e5",0)
    default_var("e5e6",0)
    default_var("e5i2",0)
    default_var("e5i6",0)
    default_var("e6e2",0)
    default_var("e6e4",0)
    default_var("e6e5",0)
    default_var("e6e6",0)
    default_var("e6i2",0)
    default_var("e6i6",0)
    default_var("e6rt",0)
    default_var("e6tc",0)
    default_var("i2e2",0)
    default_var("i2e4",0)
    default_var("i2e5",0)
    default_var("i2e6",0)
    default_var("i2i2",0)
    default_var("i2i6",0)
    default_var("i6e4",0)
    default_var("i6e5",0)
    default_var("i6e6",0)
    default_var("i6i6",0)
    default_var("rtrt",0)
    default_var("rttc",0)
    default_var("tce2",0)
    default_var("tce4",0)
    default_var("tce5",0)
    default_var("tce6",0)
    default_var("tci2",0)
    default_var("tci6",0)
    default_var("tcrt",0)
}

// midpoint set
if (parmset==4) {
    default_var("e2e2",3)
    default_var("e2e5",3)
    default_var("e2e6",3)
    default_var("e2i2",3)
    default_var("e2i6",3)
    default_var("e4e2",3)
    default_var("e4e4",3)
    default_var("e4e5",3)
    default_var("e4e6",3)
    default_var("e4i2",3)
    default_var("e4i6",3)
    default_var("e5e2",3)
    default_var("e5e4",3)
    default_var("e5e5",3)
    default_var("e5e6",3)
    default_var("e5i2",3)
    default_var("e5i6",3)
    default_var("e6e2",3)
    default_var("e6e4",3)
    default_var("e6e5",3)
    default_var("e6e6",3)
    default_var("e6i2",3)
    default_var("e6i6",3)
    default_var("e6rt",3)
    default_var("e6tc",3)
    default_var("i2e2",3)
    default_var("i2e4",3)
    default_var("i2e5",3)
    default_var("i2e6",3)
    default_var("i2i2",3)
    default_var("i2i6",3)
    default_var("i6e4",3)
    default_var("i6e5",3)
    default_var("i6e6",3)
    default_var("i6i6",3)
    default_var("rtrt",3)
    default_var("rttc",3)
    default_var("tce2",3)
    default_var("tce4",3)
    default_var("tce5",3)
    default_var("tce6",3)
    default_var("tci2",3)
    default_var("tci6",3)
    default_var("tcrt",3)
}

use_p2c_net_connections = 0 // not 0, requires p2c emitted  map and compmap files

strdef varfn
if (Control==1) {
sprint(varfn, "control.dat")
} else {
sprint(varfn, "%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d.dat", e2e2,e2e5,e2e6,e2i2,e2i6,e4e2,e4e4,e4e5,e4e6,e4i2,e4i6,e5e2,e5e4,e5e5,e5e6,e5i2,e5i6,e6e2,e6e4,e6e5,e6e6,e6i2,e6i6,i2e2,i2e4,i2e5,i2e6,i2i2,i2i6,i6e4,i6e5,i6e6,i6i6)
}

objref tfn[12]
strdef trace
objref Jtrace[12]


if (jordan_trace == 1){
{sprint(trace, "data/traces/trace_suppyrRS_%s",varfn)}
tfn[0] = new String(trace)
{sprint(trace, "data/traces/trace_suppyrFRB_%s",varfn)}
tfn[1] = new String(trace)
{sprint(trace, "data/traces/trace_supaxax_%s",varfn)}
tfn[2] = new String(trace)
{sprint(trace, "data/traces/trace_spinstell_%s",varfn)}
tfn[3] = new String(trace)
{sprint(trace, "data/traces/trace_tuftIB_%s",varfn)}
tfn[4] = new String(trace)
{sprint(trace, "data/traces/trace_tuftRS_%s",varfn)}
tfn[5] = new String(trace)
{sprint(trace, "data/traces/trace_nontuftRS_%s",varfn)}
tfn[6] = new String(trace)
{sprint(trace, "data/traces/trace_deepaxax_%s",varfn)}
tfn[7] = new String(trace)
{sprint(trace, "data/traces/trace_deepbask_%s",varfn)}
tfn[8] = new String(trace)
{sprint(trace, "data/traces/trace_supbask_%s",varfn)}
tfn[9] = new String(trace)
{sprint(trace, "data/traces/trace_supLTS_%s",varfn)}
tfn[10] = new String(trace)
{sprint(trace, "data/traces/trace_deepLTS_%s",varfn)}
tfn[11] = new String(trace)
for i = 0, 11 {
	Jtrace[i] = new Vector()
}
}

objref EF[10]
for i = 0, 9 {
	EF[i] = new Vector()
}

objref tvec, EFtvec
tvec = new Vector()
EFtvec = new Vector()
double efmm[10]

{localloadfile("manage_setup.hoc")}

//{localloadfile("syndump.hoc")}
// quit()

steps_per_ms = 40
dt = .025
secondorder = 2
default_var("mytstop", 3000)
tstop = mytstop


//{load_file("balanal.hoc")}
//if (pc.nhost >= 128) {thread_per_piece()}

if (0) { pc.runworker()  pc.done() quit() }

//{finitialize(-65) cvode_local(1) cvode.atol(1e-4)} // the finitialze avoids /0 in BREAKPOINT

prun()

//if (pc.nhost >= 128) {balanalfile("balanal.dat")}

endtime = startsw()

if (pc.id == 0) { print "tstop = ", tstop }
if (pc.id == 0) { print "RunTime: ", runtime }

//{localloadfile("prcellstate.hoc")}
proc pcs() {local spgid
	spgid = thishost_gid($1)
	if (spgid >= 0) prcellstate(load_balance_phase, spgid)
	pc.runworker()  pc.done() quit()
}
//pcs(103)


// if (pc.nhost > 5) {cvode_active(1)} // to count equations
{pc.runworker()}

print "Maximum integration interval: ", mindelay()
getstat()
prhist()
//print_spike_stat_info()

{pc.done()}

perf2file()
endtime = startsw() - endtime
print "endtime ", endtime

if (!serial) { quit() }

Loading data, please wait...