// Just load the neuron model, without reloading the MRF
load_file("nrngui.hoc")
strdef somaname,stimname
somaname="pyr3_.comp[1].v(0.5)"
stimname="pyr3_.inj1_.amp"
load_file("model/pyr3_template")
objref pyr3_
pyr3_ = new pyr3(5,CELL)
dt = 0.025
step_per_ms = 40
tstop = 2015
v_init = -70
// from setup/setupParameters.hoc
// Initializing dummy parameters and loading procs to insert these into the model
dphi_cad = 52 / 2e-3
dbeta_cad = 1 / 100 // in the paper beta = 50 [ms]
dgnaf = 0.2501575996 // tuned NernstTest12 // 0.312 // tuned 84 // 150e-3 * 1.25 // default
dgkdr = 0.0513842372 // tuned NernstTest12 // 1.554 // tuned 84 // 125e-3
dgka = 0
dgk2 = 0
dgkm = 0.0016943554 // tuned NernstTest12 // 0.00138 // tuned 84 // 2.5 * 1.5e-3 * 2
dgkc = 0
dgkahp = 0
dgcad = 0
dgnap = 0
dgcat = 0
dgcal = 0
// Passive parameters
if ( CELL == 2) {
// young cell passive parameters // tuned papernew/young_sub/ihold_0_80_160/
dgar = 2.83162e-05 // 1e-10
dg_pas = 3.95094e-05 // 9.0916e-05
de_pas = -67.92914 // -69.9598
dcm = 1.09243 // 1.0 // (manual) // 0.9 //(default)
} else if ( CELL == 3 ) {
// aged cell passive parameters // tuned papernew/aged_sub/
dgar = 3.61324e-05 // 5.0560e-05
dg_pas = 1.71951e-05 // 1.7479e-05
de_pas = -76.7721 // -79.9509
dcm = 0.70449 // 1.0 // (manual) // 0.9 //(default)
}
//dgar = 1e-10 // (optimised) // 0.25e-03 //(default)
//dg_pas = 9.0916e-05 //tuned 2stage pt 1 SO // 0.0000514733 // tuned NernstTest12 // 0.0000558 // tuned 84 // 0.00014829 // (optimised) // 0.000056 // kin opt // 2e-05 //(default)
//de_pas = -69.9598 // tuned 2stage pt 1 SO //-65.792 // (optimised) //-70 // (default)
dRa = 150 // (manual) // 250 //(default)
dena = 65.204611 // using nernst( 115 , 5 , 1 ) // 50 // default
dek = -75.497 // using nernst( 115 , 5 , 1 ) // -95 // default
// kinetics parameters
// if a taumod != 1, usetable gets turned off in set_taumods()
// taumods
dtmmnaf = 1 // default
dtmhnaf = 1 // default
dtmkdr = 1 // default
dtmkm = 1 // default
dtmkc = 1 // default
dtmcal = 1 // default
dtmmka = 1 // default
dtmhka = 1 // default
dtmnap = 1 // default
dtmar = 1 // default
// vshifts
dvsnaf = -3.5 // default
dvskdr = 0 // default
dvskm = 0 // default
dvskc = 0 // default
dvscal = 0 // default
dvska = 0 // default
dvsnap = 0 // default
dvsar = 0 // default
/***************************************************************
* Use set_conds() and set_kins() to adjust specific sections of
* model based on what needs to be changed in each compartment.
* Uses dummy values set up by the parameter names, and scales
* them according to the compartment being inserted into...
* Values set in the dummies are always for the soma, values
* everywhere else will be some scale factor of that.
* This function needs to be adjusted if the parameters being
* modified are changed.
**************************************************************/
proc set_conds() {
forsec pyr3[0].Soma {
phi_cad = dphi_cad
beta_cad = dbeta_cad
gbar_naf = dgnaf
gbar_kdr = dgkdr
gbar_ka = dgka
gbar_k2 = dgk2
gbar_ar = dgar
gbar_kc = 1.6 * dgkc //dkc * dgkc // in tha paper 'dkc * 12e-3'
gbar_kahp = dgkahp
gbar_km = dgkm
gbar_cad = dgcad
gbar_nap = dgnap
gbar_cat = dgcat
gbar_cal = dgcal
g_pas = dg_pas
e_pas = de_pas
Ra = dRa
cm = dcm
ena = dena
ek = dek
}
forsec pyr3[0].Dendrites {
phi_cad = dphi_cad
beta_cad = dbeta_cad*5
gbar_naf = dgnaf*0.03333
gbar_kdr = 0
gbar_ka = dgka*0.06667
gbar_k2 = dgk2
gbar_ar = dgar
gbar_kc = 0
gbar_kahp = dgkahp
gbar_km = dgkm
gbar_cad = dgcad
gbar_nap = dgnap
gbar_cat = dgcat
gbar_cal = dgcal
g_pas = dg_pas
e_pas = de_pas
Ra = dRa
cm = dcm
ena = dena
ek = dek
}
forsec pyr3[0].Axon {
gbar_naf = dgnaf*2.133
gbar_kdr = dgkdr*3.2
gbar_ka = dgka/15
gbar_k2 = dgk2
g_pas = dg_pas*50
e_pas = de_pas
Ra = dRa*0.4
cm = dcm
ena = dena
ek = dek
}
forsec pyr3[0].Prox {
gbar_naf = dgnaf*0.5
gbar_kdr = dgkdr*0.75
}
pyr3[0].comp[38] {
gbar_ka = dgka
gbar_naf = dgnaf*0.66667
gbar_kdr = dgkdr*0.75
}
}
// Set kinetic parameters:
proc set_kins() {
// set taumod values to the optimiser values
mtaumod_naf = dtmmnaf
htaumod_naf = dtmhnaf
taumod_kdr = dtmkdr
taumod_km = dtmkm
taumod_kc = dtmkc
taumod_cal = dtmcal
mtaumod_ka = dtmmka
htaumod_ka = dtmhka
taumod_nap = dtmnap
taumod_ar = dtmar
// set usetable values to 0 if needed
if ( mtaumod_naf != 1 ) { usetable_naf = 0 }
if ( htaumod_naf != 1 ) { usetable_naf = 0 }
if ( taumod_kdr != 1 ) { usetable_kdr = 0 }
if ( taumod_km != 1 ) { usetable_km = 0 }
if ( taumod_kc != 1 ) { usetable_kc = 0 }
if ( taumod_cal != 1 ) {usetable_cal = 0 }
if ( mtaumod_ka != 1 ) { usetable_ka = 0 }
if ( htaumod_ka != 1 ) { usetable_ka = 0 }
if ( usetable_nap != 1 ) {usetable_nap = 0 }
if ( usetable_ar != 1 ) {usetable_ar = 0 }
// vshifts:
fastNashift_naf = dvsnaf
vshift_kdr = dvskdr
vshift_km = dvskm
vshift_kc = dvskc
vshift_cal = dvscal
vshift_ka = dvska
vshift_nap = dvsnap
vshift_ar = dvsar
// set usetable values to 0 if needed
if ( fastNashift_naf != -3.5 ) { usetable_naf = 0 }
if ( vshift_kdr != 0 ) { usetable_kdr = 0 }
if ( vshift_km != 0 ) { usetable_km = 0 }
if ( vshift_kc != 0 ) { usetable_kc = 0 }
if ( vshift_cal != 0 ) {usetable_cal = 0 }
if ( vshift_ka != 0 ) {usetable_ka = 0 }
if ( vshift_nap != 0 ) {usetable_nap = 0 }
if ( vshift_ar != 0 ) {usetable_ar = 0 }
}
NP = 23 // all parameters used in simulations in the paper
set_conds()
set_kins()
//pyr3_.unset_active()
INITDUR = 50
V0 = -70
if (CELL == 2) {
V0 = -70
} else if (CELL == 3) {
V0 = -68.5
}
xopen("custominit.hoc")
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