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hocfromstr.py
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390 lines (336 loc) · 16.5 KB
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#hoc from string
class optimizedhoc(object):
def __init__(self,
listofparams,
condition):
self.listofparams = listofparams
self.condition = condition
self.oh()
def oh(self):
gc = """/********************** GRANULE CELL ****************************************
// extracted from
// Dentate gyrus network model
// Santhakumar V, Aradi I, Soltesz I (2005) J Neurophysiol 93:437-53
// https://senselab.med.yale.edu/ModelDB/showModel.cshtml?model=51781&file=\dentategyrusnet2005\DG500_M7.hoc
// ModelDB file along with publication:
// Yim MY, Hanuschkin A, Wolfart J (2015) Hippocampus 25:297-308.
// http://onlinelibrary.wiley.com/doi/10.1002/hipo.22373/abstract
// modified and augmented by
// Abraham Nunes / 2022
// Man Yi Yim / 2015
// Alexander Hanuschkin / 2011
TODO:
- Pass ndend1/2 as arguments
- Allow for creation of more than just 2 dendrites
*/
begintemplate GranuleCell
ndend1=4
ndend2=4
public pre_list, connect_pre, subsets, is_art, is_connected
public vbc2gc, vmc2gc, vhc2gc, vgc2bc, vbc2bc, vmc2bc, vhc2bc, vgc2mc, vbc2mc, vmc2mc, vhc2mc, vgc2hc, vmc2hc
public soma, gcdend1, gcdend2
public all, gcldend, pdend, mdend, ddend
objref all, gcldend, pdend, mdend, ddend
create soma, gcdend1[ndend1], gcdend2[ndend2]
objref syn, pre_list
//to include steady state current injection
nst=1
objectvar stim[nst]
public stim
// double stimdur[nst], stimdel[nst], stimamp[nst]
// public stim, stimdur, stimamp, stimdel
proc init() {
// Process input arguments
// This is ridiculous. There must be a cleaner way. [ TODO ]
narg = numarg()
cell_index = $1
scale_ka_conductances = 1
scale_km_conductances = 1
gbar_ht_ = 0
gbar_lt_ = 0
scale_size_ = 1
scale_gabaa_ = 1
scale_kir_ = 0
if (narg > 1) { scale_ka_conductances = $2 }
if (narg > 2) { scale_km_conductances = $3 }
if (narg > 3) { gbar_ht_ = $4 }
if (narg > 4) { gbar_lt_ = $5 }
if (narg > 5) { scale_size_ = $6 }
if (narg > 6) { scale_gabaa_ = $7 }
if (narg > 7) { scale_kir_ = $8 }
// Run actual initialization
pre_list = new List()
subsets()
gctemp()
synapse()
}
proc subsets(){ local i
all = new SectionList()
soma all.append()
for i=0, 3 gcdend1 [i] all.append()
for i=0, 3 gcdend2 [i] all.append()
gcldend = new SectionList()
gcdend1 [0] gcldend.append()
gcdend2 [0] gcldend.append()
pdend = new SectionList()
gcdend1 [1] pdend.append()
gcdend2 [1] pdend.append()
mdend = new SectionList()
gcdend1 [2] mdend.append()
gcdend2 [2] mdend.append()
ddend = new SectionList()
gcdend1 [3] ddend.append()
gcdend2 [3] ddend.append()
}
proc gctemp() {
scale_area = 1./1.13 * scale_size_
// ********** Parameters for reversal potentials (assigned below) *********
e_gabaa_ = -70. // reversal potential GABAA
// ***************** Parameters
g_pas_fit_ = 1.44e-05
gkbar_kir_fit_ = 1.44e-05 * scale_kir_
ggabaabar_fit_ = 0.722e-05 * scale_gabaa_
// *********************** PAS ******************************************
cm_fit_ = 1.
Ra_fit_ = 184. // fitted
// *********************** KIR *****************************************
vhalfl_kir_fit_ = -98.923594 // for Botzman I/V curve, fitted
kl_kir_fit_ = 10.888538 // for Botzman I/V curve, fitted
q10_kir_fit_ = 1. // temperature factor, set to 1
vhalft_kir_fit_ = 67.0828 // 3 values for tau func from Stegen et al. 2011
at_kir_fit_ = 0.00610779
bt_kir_fit_ = 0.0817741
// ********************* Neuron Morphology etc ***************************
LJP_ = -10. // Liquid junction potential [mV]
V_rest = -68.16+LJP_ // resting potential [mV]
V_init = -68.16+LJP_ // initial potential [mV]
// ******************** GABAA ********************
e_pas_fit_ = -83.8
e_pas_fit_Dend = -81.74
soma {nseg=1 L=16.8*scale_area diam=16.8*scale_area} // changed L & diam
gcdend1 [0] {nseg=1 L=50*scale_area diam=3*scale_area}
for i = 1, 3 gcdend1 [i] {nseg=1 L=150*scale_area diam=3*scale_area}
gcdend2 [0] {nseg=1 L=50*scale_area diam=3*scale_area}
for i = 1, 3 gcdend2 [i] {nseg=1 L=150*scale_area diam=3*scale_area}
forsec all {
insert ccanl
catau_ccanl = 10
caiinf_ccanl = 5.e-6
insert HT
gbar_HT = gbar_ht_
kan_HT = 0.5
kbn_HT = 0.3
insert LT
gbar_LT = gbar_lt_
Ra=Ra_fit_
}
soma {insert bk
gkbar_bk = %.20f // fitted to iPSC [SS]
insert ichan2
gnatbar_ichan2 = %.20f // fitted to iPSC [SS]
el_ichan2 = e_pas_fit_ // set leak reversal poti to gain Vrest of cell <ah>
vshiftma_ichan2 = %.20f // fitted to iPSC [SS]
vshiftmb_ichan2 = %.20f // fitted to iPSC [SS]
vshiftha_ichan2 = %.20f // fitted to iPSC [SS]
vshifthb_ichan2 = %.20f // fitted to iPSC [SS]
vshiftnfa_ichan2 = %.20f // fitted to iPSC [SS]
vshiftnfb_ichan2 = %.20f // fitted to iPSC [SS]
vshiftnsa_ichan2 = %.20f // fitted to iPSC [SS]
vshiftnsb_ichan2 = %.20f // fitted to iPSC [SS]
gkfbar_ichan2 = %.20f // fitted to iPSC [SS]
gksbar_ichan2 = %.20f // fitted to iPSC [SS]
gl_ichan2 = %.20f // fitted to iPSC [SS]
insert lca
glcabar_lca = %.20f // fitted to iPSC [SS]
insert nca
gncabar_nca = %.20f // fitted to iPSC [SS]
insert sk
gskbar_sk = %.20f // fitted to iPSC [SS]
insert tca
gcatbar_tca = %.20f // fitted to iPSC [SS]
insert ka
gkabar_ka = 0.012 * scale_ka_conductances // Yim et al.
insert km
gbar_km = 0.001 * scale_km_conductances // Yim et al.
cm=cm_fit_
}
forsec gcldend {
// all values fitted to iPSC except cm [SS]
insert bk
gkbar_bk = %.20f
insert ichan2
gnatbar_ichan2 = %.20f
el_ichan2 = e_pas_fit_ // set leak reversal poti to gain Vrest of cell <ah>
vshiftma_ichan2 = %.20f
vshiftmb_ichan2 = %.20f
vshiftha_ichan2 = %.20f
vshifthb_ichan2 = %.20f
vshiftnfa_ichan2 = %.20f
vshiftnfb_ichan2 = %.20f
vshiftnsa_ichan2 = %.20f
vshiftnsb_ichan2 = %.20f
gkfbar_ichan2 = %.20f
gksbar_ichan2 = %.20f
gl_ichan2 = %.20f
insert lca
glcabar_lca = %.20f
insert nca
gncabar_nca = %.20f
insert sk
gskbar_sk = %.20f
insert tca
gcatbar_tca = %.20f
cm=cm_fit_
}
forsec pdend {
// all values fitted to iPSC except cm [SS]
insert bk
gkbar_bk = %.20f
insert ichan2
gnatbar_ichan2 = %.20f
el_ichan2 = e_pas_fit_ // set leak reversal poti to gain Vrest of cell <ah>
vshiftma_ichan2 = %.20f
vshiftmb_ichan2 = %.20f
vshiftha_ichan2 = %.20f
vshifthb_ichan2 = %.20f
vshiftnfa_ichan2 = %.20f
vshiftnfb_ichan2 = %.20f
vshiftnsa_ichan2 = %.20f
vshiftnsb_ichan2 = %.20f
gkfbar_ichan2 = %.20f
gksbar_ichan2 = %.20f
gl_ichan2 = %.20f
insert lca
glcabar_lca = %.20f
insert nca
gncabar_nca = %.20f
insert sk
gskbar_sk = %.20f
insert tca
gcatbar_tca = %.20f
cm=cm_fit_*1.6
}
forsec mdend {
// all values fitted to iPSC except cm [SS]
insert bk
gkbar_bk = %.20f
insert ichan2
gnatbar_ichan2 = %.20f
el_ichan2 = e_pas_fit_ // set leak reversal poti to gain Vrest of cell <ah>
vshiftma_ichan2 = %.20f
vshiftmb_ichan2 = %.20f
vshiftha_ichan2 = %.20f
vshifthb_ichan2 = %.20f
vshiftnfa_ichan2 = %.20f
vshiftnfb_ichan2 = %.20f
vshiftnsa_ichan2 = %.20f
vshiftnsb_ichan2 = %.20f
gkfbar_ichan2 = %.20f
gksbar_ichan2 = %.20f
gl_ichan2 = %.20f
insert lca
glcabar_lca = %.20f
insert nca
gncabar_nca = %.20f
insert sk
gskbar_sk = %.20f
insert tca
gcatbar_tca = %.20f
cm=cm_fit_*1.6
}
forsec ddend {
// all values fitted to iPSC except cm [SS]
insert bk
gkbar_bk = %.20f
insert ichan2
gnatbar_ichan2 = %.20f
el_ichan2 = e_pas_fit_ // set leak reversal poti to gain Vrest of cell <ah>
vshiftma_ichan2 = %.20f
vshiftmb_ichan2 = %.20f
vshiftha_ichan2 = %.20f
vshifthb_ichan2 = %.20f
vshiftnfa_ichan2 = %.20f
vshiftnfb_ichan2 = %.20f
vshiftnsa_ichan2 = %.20f
vshiftnsb_ichan2 = %.20f
gkfbar_ichan2 = %.20f
gksbar_ichan2 = %.20f
gl_ichan2 = %.20f
insert lca
glcabar_lca = %.20f
insert nca
gncabar_nca = %.20f
insert sk
gskbar_sk = %.20f
insert tca
gcatbar_tca = %.20f
cm=cm_fit_*1.6
}
connect gcdend1[0](0), soma(1)
connect gcdend2[0](0), soma(1)
for i=1,3 {
connect gcdend1[i](0), gcdend1[i-1](1)
}
for i=1,3 {
connect gcdend2[i](0), gcdend2[i-1](1)
}
forsec all {
insert kir // kir conductance added in Yim et al. 2015, note that eK=-90mV is used instead of -105mV as reported in the paper <ah>
gkbar_kir = gkbar_kir_fit_
vhalfl_kir = vhalfl_kir_fit_
kl_kir = kl_kir_fit_
vhalft_kir = vhalft_kir_fit_
at_kir = at_kir_fit_
bt_kir = bt_kir_fit_
ggabaa_ichan2 = ggabaabar_fit_ // added GabaA in Yim et al. 2015 <ah>
egabaa_ichan2 = e_gabaa_ // reversal potential GABAA added in Yim et al. 2015 <ah>
ena = 50 // ena was unified from enat=55 (BC, HIPP, MC) and enat=45 (GC) in Santhakumar et al. (2005) <ah>
ek = -90 // simplified ekf=eks=ek=esk; note the eK was erroneously reported as -105mV in the Yim et al. 2015 <ah>
cao_ccanl = 2 }
} // end of gctemp()
// Retrieval of objref arguments uses the syntax: $o1, $o2, ..., $oi.
// http://web.mit.edu/neuron_v7.1/doc/help/neuron/general/ocsyntax.html#arguments
proc connect_pre() {
soma $o2 = new NetCon (&v(1), $o1)
}
// Define synapses on to GCs using
//- an Exp2Syn object (parameters tau1 -rise, tau2 -decay,
// time constant [ms] and e - rev potential [mV]
// delay [ms] and weight -variable betw 0 and 1 [1 corresponding to 1 'S]
proc synapse() {
gcdend1[3] syn = new Exp2Syn(0.5) // PP syn based on data from Greg Hollrigel and Kevin Staley <AH> NOTE: both synapses are identical!
syn.tau1 = 1.5 syn.tau2 = 5.5 syn.e = 0
pre_list.append(syn)
gcdend2[3] syn = new Exp2Syn(0.5) // PP syn based on Greg and Staley
syn.tau1 = 1.5 syn.tau2 = 5.5 syn.e = 0
pre_list.append(syn)
gcdend1[1] syn = new Exp2Syn(0.5) // MC syn *** Estimated
syn.tau1 = 1.5 syn.tau2 = 5.5 syn.e = 0
pre_list.append(syn)
gcdend2[1] syn = new Exp2Syn(0.5) // MC syn *** Estimated
syn.tau1 = 1.5 syn.tau2 = 5.5 syn.e = 0
pre_list.append(syn)
gcdend1[3] syn = new Exp2Syn(0.5) // HIPP syn based on Harney and Jones corrected for temp
syn.tau1 = 0.5 syn.tau2 = 6 syn.e = -70
pre_list.append(syn)
gcdend2[3] syn = new Exp2Syn(0.5) // HIPP syn based on Harney and Jones corrected for temp
syn.tau1 = 0.5 syn.tau2 = 6 syn.e = -70
pre_list.append(syn)
soma syn = new Exp2Syn(0.5) // BC syn based on Bartos
syn.tau1 = 0.26 syn.tau2 = 5.5 syn.e = -70
pre_list.append(syn)
gcdend1[1] syn = new Exp2Syn(0.5) // NOTE: SPROUTED SYNAPSE based on Molnar and Nadler
syn.tau1 = 1.5 syn.tau2 = 5.5 syn.e = 0
pre_list.append(syn)
gcdend2[1] syn = new Exp2Syn(0.5) // NOTE: SPROUTED SYNAPSE
syn.tau1 = 1.5 syn.tau2 = 5.5 syn.e = 0
pre_list.append(syn)
// Total of 7 synapses per GC 0,1 PP; 2,3 MC; 4,5 HIPP and 6 BC 7,8 Sprout
}
func is_art() { return 0 }
endtemplate GranuleCell
""" %tuple(self.listofparams)
filename = "GC_%s" %self.condition
hocfile = open("objects/%s.hoc" %filename, "w")
hocfile.write(gc)
hocfile.close()