//xopen("$(NEURONHOME)/lib/hoc/noload.hoc")
//pwman_place(20,21)
begintemplate MelnickSG
ndend=1
public soma, hillock, axon, dend
public synlist, x, y, z, position, connect2target
objref synlist, syn_
create soma, hillock, axon, dend
proc init(){
access soma
{diam=10 L=10 nseg=10} // area 100 um2 means mA/cm2 identical to nA
insert B_Na
insert B_A
insert B_DR
insert KDR
insert KDRI
insert pas
{gnabar_B_Na = 0.008 ena = 60 g_pas = 1.1e-05 e_pas = -70 gkbar_KDRI = 0.0043 ek = -84}
access hillock
{L=30 nseg=30 dsoma=1 daxon=0.5 diam(0:1)=dsoma:daxon}
insert B_Na
insert B_A
insert B_DR
insert KDR
insert KDRI
insert pas
{gnabar_B_Na = 3.45 ena = 60 g_pas = 1.1e-05 e_pas = -70 gkbar_KDRI = 0.076 ek = -84} // Tonic firing with maintained I-F characteristics.
access axon
{diam=0.001 L=0.001 nseg=50}
insert B_Na
insert B_A
insert B_DR
insert KDR
insert KDRI
insert pas
{gnar_B_Na = 0 ena = 60 g_pas = 0 e_pas = -70 gkbar_KDRI = 0 ek = -84}
access dend
{nseg=50 diam=1.4 L = 1371}
// diam(0.43:1) = 4:0 // tapering of the distal dendrite
//insert B_Na
insert SS
insert B_DR
insert KDR
insert KDRI
insert pas
{gnabar_SS = 0 ena = 60 g_pas = 1.1e-05 e_pas = -70 gkbar_KDRI = 0.034 ek = -84}
soma connect hillock(0),1
hillock connect axon(0),1
soma connect dend(0),0
forall Ra = 80
synlist = new List()
synapses()
x = y = z = 0
}
objref SynapseID, SynapseFile, NumVec
strdef SynapseIDFile
proc synapses(){
SynapseFile = new File()
SynapseID = new File()
SynapseID.ropen("SG_Cell_SynapseID.dat")
SynapseID.scanstr(SynapseIDFile)
SynapseID.close()
NumVec = new Vector()
SynapseFile.ropen(SynapseIDFile)
NumVec.scantil(SynapseFile, -1e15)
SynapseFile.close()
for num = 0, NumVec.x[0]-1{
dend syn_ = new AMPA_DynSyn(0.5) syn_.tau_rise = 0.1 syn_.tau_decay = 5 synlist.append(syn_)
}
for num = 0, NumVec.x[1]-1{
dend syn_ = new AMPA_DynSyn(0.5) syn_.tau_rise = 0.1 syn_.tau_decay = 5 synlist.append(syn_)
}
}
proc position() { local i
soma for i = 0, n3d()-1 {
pt3dchange(i, $1-x+x3d(i), $2-y+y3d(i), $3-z+z3d(i), diam3d(i))
}
x = $1 y = $2 z = $3
}
obfunc connect2target() { localobj nc //$o1 target point process, optional $o2 returned NetCon
soma nc = new NetCon(&v(1), $o1)
nc.threshold = -30
if (numarg() == 2) { $o2 = nc } // for backward compatibility
return nc
}
endtemplate MelnickSG
//*NEW TEMPLATE*//
//*NEW TEMPLATE*//
//*NEW TEMPLATE*//
begintemplate AguiarIN
public soma, dend, hillock, axon, synlist, x, y, z, position, connect2target
create soma, dend, hillock, axon
objref synlist, syn_
proc init() {
x = y = z = 0
create soma
soma {
nseg = 3
L = 20.0
diam = 20.0
//HH channels: iNat and iK
insert HH2 {
gnabar_HH2 = 0.08
gkbar_HH2 = 0.02
vtraub_HH2 = -55.0
}
//intracellular Ca dynamics
insert CaIntraCellDyn {
depth_CaIntraCellDyn = 0.1
cai_tau_CaIntraCellDyn = 1.0
cai_inf_CaIntraCellDyn = 50.0e-6
}
//potassium current dependent on intracellular calcium concentration
insert iKCa {
gbar_iKCa = 0.002 //0.002
}
ek = -70.0
Ra = 150.0
insert pas
g_pas = 4.2e-5
e_pas = -65.0
}
create dend
dend {
nseg = 5
L = 500.0
diam = 6.0
//intracellular Ca dynamics
insert CaIntraCellDyn {
depth_CaIntraCellDyn = 0.1
cai_tau_CaIntraCellDyn = 2.0
cai_inf_CaIntraCellDyn = 50.0e-6
}
//HH channels: iNat and iK
//NORMALLy not there.
insert HH2{
gnabar_HH2 = 0.000
gkbar_HH2 = 0.036 // *5/6
}
//potassium current dependent on intracellular calcium concentration
insert iKCa {
gbar_iKCa = 0.002 //0.002
}
ek = -70.0
Ra = 150.0
insert pas
g_pas = 4.2e-5
e_pas = -65.0
}
create hillock
hillock {
nseg = 3
L = 3.0
diam(0:1) = 2.0:1.0
//HH channels: iNa,t and iK
insert HH2 {
gnabar_HH2 = 5
gkbar_HH2 = 0.076*5/24
vtraub_HH2 = -55.0
}
Ra = 150.0
insert pas
g_pas = 4.2e-5
e_pas = -65.0
}
create axon
axon {
nseg = 5
L = 1000.0
diam = 1.0
//HH channels: iNa,t and iK
insert HH2 {
gnabar_HH2 = 0.1
gkbar_HH2 = 0.04 //0.06
vtraub_HH2 = -55
}
Ra = 150.0
insert pas
g_pas = 4.2e-5
e_pas = -65.0
}
//CONNECTIONS
soma connect hillock(0),1
hillock connect axon(0),1
soma connect dend(0),0
synlist = new List()
synapses()
}
proc position() { local i
soma for i = 0, n3d()-1 {
pt3dchange(i, $1-x+x3d(i), $2-y+y3d(i), $3-z+z3d(i), diam3d(i))
}
x = $1 y = $2 z = $3
}
obfunc connect2target() { localobj nc //$o1 target point process, optional $o2 returned NetCon
soma nc = new NetCon(&v(1), $o1)
nc.threshold = -30
if (numarg() == 2) { $o2 = nc } // for backward compatibility
return nc
}
objref SynapseID, SynapseFile, NumVec
strdef SynapseIDFile
proc synapses(){
SynapseFile = new File()
SynapseID = new File()
SynapseID.ropen("IN_Cell_SynapseID.dat")
SynapseID.scanstr(SynapseIDFile)
SynapseID.close()
NumVec = new Vector()
SynapseFile.ropen(SynapseIDFile)
NumVec.scantil(SynapseFile, -1e15)
SynapseFile.close()
for num = 0, 29{
dend syn_ = new AMPA_DynSyn(0.5) syn_.tau_rise = 0.1 syn_.tau_decay = 5 synlist.append(syn_)
}
for num = 0, 29{
dend syn_ = new NMDA_DynSyn(0.5) syn_.tau_rise = 2 syn_.tau_decay = 100 synlist.append(syn_)
}
for num = 0, 29{
dend syn_ = new NK1_DynSyn(0.5) syn_.tau_rise = 100 syn_.tau_decay = 3000 synlist.append(syn_)
}
for num = 0, 1{
dend syn_ = new GABAa_DynSyn(0.5) syn_.tau_rise = 0.1 syn_.tau_decay = 20 synlist.append(syn_)
}
}
endtemplate AguiarIN
//*NEW TEMPLATE*//
//*NEW TEMPLATE*//
//*NEW TEMPLATE*//
//Created by Paulo Aguiar [pauloaguiar@fc.up.pt]
// CREATE WDR NEURON
begintemplate AguiarWDR
public soma, dend, hillock, axon, x, y, z, position, connect2target
public synlist
objref syn_, synlist
create soma, dend, hillock, axon
proc init() {
x = y = z = 0
cascale = 1.5
create soma
soma {
nseg = 3
L = 20.0
diam = 20.0
//HH channels: iNat and iK
insert HH2 { //No AP Initiation in the soma?
gnabar_HH2 = 0.000 //"Default" 0.08. Melnick 0.008.
gkbar_HH2 = 0.0043*5/24 //0.3e-3 in P&D. "/4" is there in parallel with Safronov.
vtraub_HH2 = -55.0
}
//intracellular Ca dynamics
insert CaIntraCellDyn {
depth_CaIntraCellDyn = 0.1
cai_tau_CaIntraCellDyn = 1.0
cai_inf_CaIntraCellDyn = 50.0e-6
}
//high-voltage activated long-lasting calcium current, L-type
insert iCaL {
pcabar_iCaL = 0.0001 * cascale//0.0001- IMPORTANT: this current drives the (activity control) somatic iKCa current
}
//non-specific current dependent on intracellular calcium concentration
insert iCaAN {
gbar_iCaAN = 0.0000 //0.00000
}
//potassium current dependent on intracellular calcium concentration
insert iKCa {
gbar_iKCa = 0.0001 * cascale * 0.1 //0.0001
}
//sodium persistent current
insert iNaP {
gnabar_iNaP = 0.0001 * cascale//0.0001
}
insert B_A{
gkbar_B_A = 0// Arbitrary value
}
insert pas{
g_pas = 4.2e-5
e_pas = -65.0
}
ek = -70.0
Ra = 150.0
}
create dend
dend {
nseg = 5
L = 500.0
diam = 6.0
//intracellular Ca dynamics
insert CaIntraCellDyn {
depth_CaIntraCellDyn = 0.1
cai_tau_CaIntraCellDyn = 2.0
cai_inf_CaIntraCellDyn = 50.0e-6
}
//high-voltage activated long-lasting calcium current, L-type
insert iCaL {
pcabar_iCaL = 3e-5 * cascale //3.0e-5 IMPORTANT: this current is important for activity control (drives the iKCa current)
}
//non-specific current dependent on intracellular calcium concentration
insert iCaAN {
gbar_iCaAN = 0.00007 * cascale//0.00007; This is a sensible parameter
//higher values of gbar_iCaAN produce graphs similar to Silviloti et al 93
}
//potassium current dependent on intracellular calcium concentration
insert iKCa {
gbar_iKCa = 0.001 * cascale//0.001; higher values place "holes" in the scatter plot, resulting from the cai bump after synaptic activation);
//naturally, lower values will lead to increased firing
}
//NORMALLy not there.
insert HH2{
gnabar_HH2 = 0.000
gkbar_HH2 = 0.036 // *5/6
}
insert pas{
g_pas = 4.2e-5
e_pas = -65.0
}
ek = -70.0
Ra = 150.0
}
create hillock
hillock {
nseg = 3
L = 3
diam(0:1) = 2.0:1.0
//HH channels: iNa,t and iK
insert HH2 {
gnabar_HH2 = 5 //Remember Melnick is 3.45. "/4" is for surface area compensation.
gkbar_HH2 = 0.076*5/24 // Default 0.04
vtraub_HH2 = -55.0
}
insert B_A{
gkbar_B_A = 0.0 // 0.036 Old Safronov Default.
}
insert pas{
g_pas = 4.2e-5
e_pas = -65.0
}
Ra = 150.0
}
create axon
axon {
nseg = 5
L = 1000 // 1000.0
diam = 1.0
//HH channels: iNa,t and iK
insert HH2 {
gnabar_HH2 = 0 //0.1
gkbar_HH2 = 0 //0.04
vtraub_HH2 = -55
}
insert pas{
g_pas = 0
e_pas = -65.0
}
Ra = 150.0
}
//CONNECTIONS
soma connect hillock(0),1
hillock connect axon(0),1
soma connect dend(0),0
//MAKE SYNAPSES HERE (DENDRITE) Use execute1(cmd) with syn_.thresh to set threshold. I can also get rid of WeightsVec if conductances will be set here.
synlist = new List()
synapses()
}
objref SynapseID, SynapseFile, NumVec
strdef SynapseIDFile
proc synapses(){
SynapseFile = new File()
SynapseID = new File()
SynapseID.ropen("T_Cell_SynapseID.dat")
SynapseID.scanstr(SynapseIDFile)
SynapseID.close()
NumVec = new Vector()
SynapseFile.ropen(SynapseIDFile)
NumVec.scantil(SynapseFile, -1e15)
SynapseFile.close()
for num = 0, 14{
dend syn_ = new AMPA_DynSyn(0.5) syn_.tau_rise = 0.1 syn_.tau_decay = 5 synlist.append(syn_)
}
for num = 0, 14{
dend syn_ = new NMDA_DynSyn(0.5) syn_.tau_rise = 2 syn_.tau_decay = 100 synlist.append(syn_)
}
for num = 0, 14{
dend syn_ = new AMPA_DynSyn(0.5) syn_.tau_rise = 0.1 syn_.tau_decay = 5 synlist.append(syn_)
}
for num = 0, 14{
dend syn_ = new NMDA_DynSyn(0.5) syn_.tau_rise = 2 syn_.tau_decay = 100 synlist.append(syn_)
}
for num = 0, 29{
dend syn_ = new NK1_DynSyn(0.5) syn_.tau_rise = 200 syn_.tau_decay = 3000 synlist.append(syn_)
}
for num = 0, 29{
dend syn_ = new AMPA_DynSyn(0.5) syn_.tau_rise = 0.1 syn_.tau_decay = 5 synlist.append(syn_)
}
for num = 0, 29{
dend syn_ = new NMDA_DynSyn(0.5) syn_.tau_rise = 2 syn_.tau_decay = 100 synlist.append(syn_)
}
for num = 0, 0{
dend syn_ = new Glycine_DynSyn(0.5) syn_.tau_rise = 0.1 syn_.tau_decay = 10 synlist.append(syn_)
}
for num = 0, 0{
dend syn_ = new GABAa_DynSyn(0.5) syn_.tau_rise = 0.1 syn_.tau_decay = 20 synlist.append(syn_)
}
}
proc position() { local i
soma for i = 0, n3d()-1 {
pt3dchange(i, $1-x+x3d(i), $2-y+y3d(i), $3-z+z3d(i), diam3d(i))
}
x = $1 y = $2 z = $3
}
obfunc connect2target() { localobj nc //$o1 target point process, optional $o2 returned NetCon
soma nc = new NetCon(&v(1), $o1)
nc.threshold = -30
if (numarg() == 2) { $o2 = nc } // for backward compatibility
return nc
}
endtemplate AguiarWDR
begintemplate S_NetStim //DUMMY NetStims; These are only included because Syn objects must be connected to NetCon object.
public pp, connect2target, x, y, z, position, is_art
objref pp
proc init() {
pp = new NetStim()
pp.interval = 0
pp.number = 0
pp.start = 0
}
func is_art() { return 1 }
obfunc connect2target() { localobj nc
nc = new NetCon(pp, $o1)
if (numarg() == 2) { $o2 = nc }
return nc
}
proc position(){x=$1 y=$2 z=$3}
endtemplate S_NetStim
//Network specification interface
objref cells, nclist, netcon
{cells = new List() nclist = new List()}
func cell_append() {cells.append($o1) $o1.position($2,$3,$4)
return cells.count - 1
}
func nc_append() {//srcindex, tarcelindex, synindex
if ($3 >= 0) {
netcon = cells.object($1).connect2target(cells.object($2).synlist.object($3))
netcon.weight = $4 netcon.delay = $5
}else{
netcon = cells.object($1).connect2target(cells.object($2).pp)
netcon.weight = $4 netcon.delay = $5
}
nclist.append(netcon)
return nclist.count - 1
}
//************************************************************************************
//UNITS
//Category Variable Units
//Time t [ms]
//Voltage v [mV]
//Current i [mA/cm2] (distributed) [nA] (point process)
//Concentration ko, ki, etc. [mM]
//Specific capacitance cm [uf/cm2]
//Length diam, L [um]
//Conductance g [S/cm2] (distributed) [uS] (point process)
//Cytoplasmic resistivity Ra [ohm cm]
//Resistance Ri [10E6 ohm]