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d2msn_2.py
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import sys
from neuron import h, hoc
from math import sqrt, pi, log, exp
Ra=100
ek=-94
ena=50
with open('wtd2_params.txt') as f:
for line in f:
exec(line)
h.xopen("msn_wolf_all_tau_vecs.hoc")
dgnaf_proxF = G_NAFD / G_NAF
dgnap_proxF = G_NAPD / G_NAP
dgnaf_midF = G_NAFD / G_NAF
dgnap_midF = G_NAPD / G_NAP
dgkas_midF = G_KASD / G_KAS
dgkaf_midF = G_KAFD / G_KAF
dgnaf_distF = G_NAFD / G_NAF
dgnap_distF = G_NAPD / G_NAP
dgkas_distF = G_KASD / G_KAS
dgkaf_distF = G_KAFD / G_KAF
class WTD2:
def __init__(self):
self.create_cell()
self.optimize_nseg()
self.settopo()
self.add_all()
self.geom_nseg()
self.setchannels()
def geom_nseg (self):
freq = 100 #Hz
d_lambda = 0.1
for sec in self.all:
sec.nseg = int((sec.L/(d_lambda*self.lambda_f(sec))+0.9)/2)*2 + 1
for sec in self.dist:
sec.nseg=3
for sec in self.axon:
sec.nseg=1
for sec in self.myelin:
sec.nseg=1
def lambda_f (self, section):
# these are reasonable values for most models
freq = 100
# The lowest number of n3d() is 2
if (section.n3d() < 2):
return 1e5*sqrt(section.diam/(4*pi*freq*section.Ra*section.cm))
# above was too inaccurate with large variation in 3d diameter
# so now we use all 3-d points to get a better approximate lambda
x1 = section.arc3d(0)
d1 = section.diam3d(0)
self.lam = 0
#print section, " n3d:", section.n3d(), " diam3d:", section.diam3d(0)
for i in range(section.n3d()): #h.n3d()-1
x2 = section.arc3d(i)
d2 = section.diam3d(i)
self.lam += (x2 - x1)/sqrt(d1 + d2)
x1 = x2
d1 = d2
# length of the section in units of lambda
self.lam *= sqrt(2) * 1e-5*sqrt(4*pi*freq*section.Ra*section.cm)
return section.L/self.lam
def create_cell(self):
self.soma = [h.Section(name='soma[%d]' % i) for i in xrange(1)]
self.proximal = [h.Section(name='proximal[%d]' % i) for i in xrange(6)]
self.middend = [h.Section(name='middend[%d]' % i) for i in xrange(12)]
self.distal = [h.Section(name='distal[%d]' % i) for i in xrange(26)]
self.axon = [h.Section(name='axon[%d]' % i) for i in xrange(2)]
self.myelin = [h.Section(name='myelin[%d]' % i) for i in xrange(1)]
h.pt3dclear(sec = self.soma[0])
h.pt3dadd(0,0,0,1, sec = self.soma[0])
h.pt3dadd(15,0,0,1, sec = self.soma[0])
self.proximal[0].connect(self.soma[0])
h.pt3dclear(sec = self.proximal[0])
h.pt3dadd(15,0,0,1, sec=self.proximal[0])
h.pt3dadd(45,-29,0,1, sec=self.proximal[0])
self.proximal[1].connect(self.soma[0])
h.pt3dclear(sec = self.proximal[1])
h.pt3dadd(15,0,0,1, sec=self.proximal[1])
h.pt3dadd(45,30,0,1, sec=self.proximal[1])
self.proximal[2].connect(self.soma[0])
h.pt3dclear(sec = self.proximal[2])
h.pt3dadd(0,0,0,1, sec=self.proximal[2])
h.pt3dadd(-29,-29,0,1, sec=self.proximal[2])
self.proximal[3].connect(self.soma[0])
h.pt3dclear(sec = self.proximal[3])
h.pt3dadd(0,0,0,1, sec=self.proximal[3])
h.pt3dadd(-29,30,0,1, sec=self.proximal[3])
self.proximal[4].connect(self.soma[0])
h.pt3dclear(sec = self.proximal[4])
h.pt3dadd(15,0,0,1, sec=self.proximal[4])
h.pt3dadd(45,0,0,1, sec=self.proximal[4])
self.proximal[5].connect(self.soma[0])
h.pt3dclear(sec = self.proximal[5])
h.pt3dadd(0,0,0,1, sec=self.proximal[5])
h.pt3dadd(-30,0,0,1, sec=self.proximal[5])
# Finished with proximal Now to middend
self.middend[0].connect(self.proximal[0])
h.pt3dclear(sec = self.middend[0])
h.pt3dadd(45,-29,0,1, sec=self.middend[0])
h.pt3dadd(45,-59,0,1, sec=self.middend[0])
self.middend[1].connect(self.proximal[0])
h.pt3dclear(sec = self.middend[1])
h.pt3dadd(45,-29,0,1, sec=self.middend[1])
h.pt3dadd(90,-29,0,1, sec=self.middend[1])
self.middend[2].connect(self.proximal[1])
h.pt3dclear(sec = self.middend[2])
h.pt3dadd(45,30,0,1, sec=self.middend[2])
h.pt3dadd(90,30,0,1, sec=self.middend[2])
self.middend[3].connect(self.proximal[1])
h.pt3dclear(sec = self.middend[3])
h.pt3dadd(45,30,0,1, sec=self.middend[3])
h.pt3dadd(60,75,0,1, sec=self.middend[3])
self.middend[4].connect(self.proximal[2])
h.pt3dclear(sec = self.middend[4])
h.pt3dadd(-29,-29,0,1, sec=self.middend[4])
h.pt3dadd(-44,-59,0,1, sec=self.middend[4])
self.middend[5].connect(self.proximal[2])
h.pt3dclear(sec = self.middend[5])
h.pt3dadd(-29,-29,0,1, sec=self.middend[5])
h.pt3dadd(-74,-29,0,1, sec=self.middend[5])
self.middend[6].connect(self.proximal[3])
h.pt3dclear(sec = self.middend[6])
h.pt3dadd(-29,30,0,1, sec=self.middend[6])
h.pt3dadd(-44,75,0,1, sec=self.middend[6])
self.middend[7].connect(self.proximal[3])
h.pt3dclear(sec = self.middend[7])
h.pt3dadd(-29,30,0,1, sec=self.middend[7])
h.pt3dadd(-74,30,0,1, sec=self.middend[7])
self.middend[8].connect(self.proximal[4])
h.pt3dclear(sec = self.middend[8])
h.pt3dadd(45, 0, 0, 1, sec=self.middend[8])
h.pt3dadd(75, 15, 0, 1, sec=self.middend[8])
self.middend[9].connect(self.proximal[4])
h.pt3dclear(sec = self.middend[9])
h.pt3dadd(45, 0, 0, 1, sec=self.middend[9])
h.pt3dadd(75, -15, 0, 1, sec=self.middend[9])
self.middend[10].connect(self.proximal[5])
h.pt3dclear(sec = self.middend[10])
h.pt3dadd(-30, 0, 0, 1, sec=self.middend[10])
h.pt3dadd(-60, 15, 0, 1, sec=self.middend[10])
self.middend[11].connect(self.proximal[5])
h.pt3dclear(sec = self.middend[11])
h.pt3dadd(-30, 0, 0, 1, sec=self.middend[11])
h.pt3dadd(-60, -15, 0, 1, sec=self.middend[11])
# Finished with middend Now to distal
self.distal[0].connect(self.middend[0])
h.pt3dclear(sec=self.distal[0])
h.pt3dadd(45, -59, 0, 1, sec=self.distal[0])
h.pt3dadd(30, -89, 0, 1, sec=self.distal[0])
self.distal[1].connect(self.middend[0])
h.pt3dclear(sec=self.distal[1])
h.pt3dadd(45, -59, 0, 1, sec=self.distal[1])
h.pt3dadd(75, -74, 0, 1, sec=self.distal[1])
self.distal[2].connect(self.middend[1])
h.pt3dclear(sec=self.distal[2])
h.pt3dadd(90, -29, 0, 1, sec=self.distal[2])
h.pt3dadd(120, -14, 0, 1, sec=self.distal[2])
self.distal[3].connect(self.middend[1])
h.pt3dclear(sec=self.distal[3])
h.pt3dadd(90, -29, 0, 1, sec=self.distal[3])
h.pt3dadd(120, -59, 0, 1, sec=self.distal[3])
self.distal[4].connect(self.middend[2])
h.pt3dclear(sec=self.distal[4])
h.pt3dadd(90, 30, 0, 1, sec=self.distal[4])
h.pt3dadd(120, 15, 0, 1, sec=self.distal[4])
self.distal[5].connect(self.middend[2])
h.pt3dclear(sec=self.distal[5])
h.pt3dadd(90, 30, 0, 1, sec=self.distal[5])
h.pt3dadd(105, 60, 0, 1, sec=self.distal[5])
self.distal[6].connect(self.middend[3])
h.pt3dclear(sec=self.distal[6])
h.pt3dadd(60, 75, 0, 1, sec=self.distal[6])
h.pt3dadd(90, 90, 0, 1, sec=self.distal[6])
self.distal[7].connect(self.middend[3])
h.pt3dclear(sec=self.distal[7])
h.pt3dadd(60, 75, 0, 1, sec=self.distal[7])
h.pt3dadd(45, 105, 0, 1, sec=self.distal[7])
self.distal[8].connect(self.middend[4])
h.pt3dclear(sec=self.distal[8])
h.pt3dadd(-44, -59, 0, 1, sec=self.distal[8])
h.pt3dadd(-29, -89, 0, 1, sec=self.distal[8])
self.distal[9].connect(self.middend[4])
h.pt3dclear(sec=self.distal[9])
h.pt3dadd(-44, -59, 0, 1, sec=self.distal[9])
h.pt3dadd(-89, -74, 0, 1, sec=self.distal[9])
self.distal[10].connect(self.middend[5])
h.pt3dclear(sec=self.distal[10])
h.pt3dadd(-74, -29, 0, 1, sec=self.distal[10])
h.pt3dadd(-104, -14, 0, 1, sec=self.distal[10])
self.distal[11].connect(self.middend[5])
h.pt3dclear(sec=self.distal[11])
h.pt3dadd(-74, -29, 0, 1, sec=self.distal[11])
h.pt3dadd(-104, -59, 0, 1, sec=self.distal[11])
self.distal[12].connect(self.middend[6])
h.pt3dclear(sec=self.distal[12])
h.pt3dadd(-44, 75, 0, 1, sec=self.distal[12])
h.pt3dadd(-14, 105, 0, 1, sec=self.distal[12])
self.distal[13].connect(self.middend[6])
h.pt3dclear(sec=self.distal[13])
h.pt3dadd(-44, 75, 0, 1, sec=self.distal[13])
h.pt3dadd(-74, 90, 0, 1, sec=self.distal[13])
self.distal[14].connect(self.middend[7])
h.pt3dclear(sec=self.distal[14])
h.pt3dadd(-74, 30, 0, 1, sec=self.distal[14])
h.pt3dadd(-89, 60, 0, 1, sec=self.distal[14])
self.distal[15].connect(self.middend[7])
h.pt3dclear(sec=self.distal[15])
h.pt3dadd(-74, 30, 0, 1, sec=self.distal[15])
h.pt3dadd(-104, 15, 0, 1, sec=self.distal[15])
self.distal[16].connect(self.middend[8])
h.pt3dclear(sec=self.distal[16])
h.pt3dadd(75, 15, 0, 1, sec=self.distal[16])
h.pt3dadd(90, 15, 0, 1, sec=self.distal[16])
self.distal[17].connect(self.middend[8])
h.pt3dclear(sec=self.distal[17])
h.pt3dadd(75, 15, 0, 1, sec=self.distal[17])
h.pt3dadd(90, 30, 0, 1, sec=self.distal[17])
self.distal[18].connect(self.middend[9])
h.pt3dclear(sec=self.distal[18])
h.pt3dadd(75, -15, 0, 1, sec=self.distal[18])
h.pt3dadd(90, -15, 0, 1, sec=self.distal[18])
self.distal[19].connect(self.middend[9])
h.pt3dclear(sec=self.distal[19])
h.pt3dadd(75, -15, 0, 1, sec=self.distal[19])
h.pt3dadd(90, -30, 0, 1, sec=self.distal[19])
self.distal[20].connect(self.middend[10])
h.pt3dclear(sec=self.distal[20])
h.pt3dadd(-40, 15, 0, 1, sec=self.distal[20])
h.pt3dadd(-63, 18, 0, 1, sec=self.distal[20])
self.distal[21].connect(self.middend[10])
h.pt3dclear(sec=self.distal[21])
h.pt3dadd(-60, 15, 0, 1, sec=self.distal[21])
h.pt3dadd(-75, 30, 0, 1, sec=self.distal[21])
# this is problematic!
self.distal[22].connect(self.middend[10],0.8,0)
h.pt3dclear(sec=self.distal[22])
h.pt3dadd(-54, 12, 0, 1, sec=self.distal[22])
h.pt3dadd(-69, 27, 0, 1, sec=self.distal[22])
self.distal[23].connect(self.middend[11])
h.pt3dclear(sec=self.distal[23])
h.pt3dadd(-40, 0, 0, 1, sec=self.distal[23])
h.pt3dadd(-63, -12, 0, 1, sec=self.distal[23])
self.distal[24].connect(self.middend[11])
h.pt3dclear(sec=self.distal[24])
h.pt3dadd(-40, 0, 0, 1, sec=self.distal[24])
h.pt3dadd(-63, -18, 0, 1, sec=self.distal[24])
# this is problematic
self.distal[25].connect(self.middend[11],0.8,0)
h.pt3dclear(sec=self.distal[25])
h.pt3dadd(-54, -12, 0, 1, sec=self.distal[25])
h.pt3dadd(-69, -27, 0, 1, sec=self.distal[25])
self.axon[0].connect(self.soma[0])
h.pt3dclear(sec=self.axon[0])
h.pt3dadd(7.5,0,0,1, sec=self.axon[0])
h.pt3dadd(7.5,20,0,1, sec=self.axon[0])
self.axon[1].connect(self.axon[0])
h.pt3dclear(sec=self.axon[1])
h.pt3dadd(7.5,20,0,1, sec=self.axon[1])
h.pt3dadd(7.5,50,0,1, sec=self.axon[1])
self.myelin[0].connect(self.axon[1])
h.pt3dclear(sec=self.myelin[0])
h.pt3dadd(7.5,50,0,1, sec=self.myelin[0])
h.pt3dadd(7.5,450,0,1, sec=self.myelin[0])
def optimize_nseg (self):
self.all=h.SectionList()
self.prox=h.SectionList()
self.mid=h.SectionList()
self.dist=h.SectionList()
self.all_no_axon=h.SectionList()
for section in self.soma:
self.all.append(sec=section)
self.all_no_axon.append(sec=section)
for section in self.proximal:
self.all.append(sec=section)
self.all_no_axon.append(sec=section)
self.prox.append(sec=section)
for section in self.middend:
self.all.append(sec=section)
self.all_no_axon.append(sec=section)
self.mid.append(sec=section)
for section in self.distal:
self.all.append(sec=section)
self.all_no_axon.append(sec=section)
self.dist.append(sec=section)
for section in self.axon:
self.all.append(sec=section)
for section in self.myelin:
self.all.append(sec=section)
for sec in self.all:
sec.Ra=100
sec.cm=0.900001
for sec in self.myelin:
sec.cm=0.01800002
def settopo(self):
#### set L and diam
self.soma[0].L=10.4941
self.soma[0].diam=9.5896
for sec in self.proximal:
sec.L=23.7905
sec.diam=1.2933559
for sec in self.middend:
sec.L=26.846188
sec.diam=1.2744389
for sec in self.distal:
sec.L=116.49579
sec.diam=0.90830576
self.axon[0].L=20
self.axon[0].diam=1.1875
self.axon[1].L=30
self.axon[1].diam=0.6875
self.myelin[0].L=400
self.myelin[0].diam=0.5
def add_all(self):
for sec in self.all:
sec.insert('pas')
for sec in self.all_no_axon:
sec.insert('naf')
sec.insert('nap')
sec.insert('kir')
sec.insert('kas')
sec.insert('kaf')
sec.insert('bkkca')
sec.insert('skkca')
sec.insert('kdr')
sec.insert('caldyn')
sec.insert('caL')
sec.insert('caL13')
sec.insert('cadyn')
sec.insert('can')
sec.insert('car')
sec.insert('cat')
for sec in self.axon:
sec.insert('naf')
sec.insert('nap')
sec.insert('kas')
sec.insert('kaf')
sec.insert('kdr')
def setchannels(self):
#### set pas params
for sec in self.all:
sec.g_pas=0.000105
sec.e_pas=-88.880424
#### set kir params
for sec in self.all_no_axon:
sec.qfact_kir=0.2
sec.mshift_kir=98.444215
sec.mslope_kir=8.123967
sec.gkbar_kir=0.007893
sec.cai=5.5097902e-06
sec.cao=5
sec.cali=5.5139085e-06
sec.calo=5
sec.eca=165.15653
sec.ena=50
sec.ek=-94
#### set shift and dynamic params
for sec in self.all_no_axon:
sec.mshift_kas = MSHIFT_KAS
sec.hshift_kas = HSHIFT_KAS
sec.mshift_kaf = MSHIFT_KAF
sec.hshift_kaf = HSHIFT_KAF
for sec in self.axon:
sec.mshift_naf=-10
sec.hshift_naf=-5
sec.ena=50
sec.ek=-94
for sec in self.all_no_axon:
QSCALE=0.2/0.5
sec.mqfact_naf=3*QSCALE
sec.hqfact_naf=3*QSCALE
sec.qfact_kas=9*QSCALE
sec.qfact_kaf=3*QSCALE
sec.qfact_nap=3*QSCALE
sec.qfact_kdr=0.5*QSCALE
sec.qfact_skkca = 1 * QSCALE
sec.q_bkkca = 1 * QSCALE
sec.qfact_can = 3 * QSCALE
sec.qfact_car = 3 * QSCALE
sec.qfact_cat = 3 * QSCALE
sec.qfact_caL = 3 * QSCALE
sec.qfact_caL13 = 3 * QSCALE
sec.hqfact_caL13 = 3 * QSCALE
for sec in self.axon:
QSCALE=0.2/0.5
sec.mqfact_naf=3*QSCALE
sec.hqfact_naf=3*QSCALE
sec.qfact_kas=9*QSCALE
sec.qfact_kaf=3*QSCALE
sec.qfact_nap=3*QSCALE
sec.qfact_kdr=0.5*QSCALE
##### set conductance in soma
for sec in self.soma:
# sec.gnabar_naf=0.890840924
sec.gnabar_naf=1.2738443502
# sec.gnabar_naf=0
# sec.gnabar_nap=0
sec.gnabar_nap=0.0015161014
sec.gkbar_kas=0.013754082
sec.gkbar_kaf=0.05
# sec.gkbar_kas=0
# sec.gkbar_kaf=0
sec.gkbar_kdr=0.0000228509
# sec.gkbar_kdr=0
sec.gkbar_bkkca=0.0000111911
sec.gkbar_skkca=0.01395996321
sec.pbar_caL=0.000001188
sec.pcaLbar_caL13=0.0000001017
sec.pbar_can=0.0000143303
sec.pcarbar_car=0.0000502025
sec.pcatbar_cat=0.0000007984
# sec.gkbar_bkkca=0.
# sec.gkbar_skkca=0
# sec.pbar_caL=0
# sec.pcaLbar_caL13=0
# sec.pbar_can=0
# sec.pcarbar_car=0
# sec.pcatbar_cat=0
for sec in self.prox:
# sec.gnabar_naf=round(0.890840924*dgnaf_proxF,9)
sec.gnabar_naf=1.2738443502*dgnaf_proxF
# sec.gnabar_naf=0
# sec.gnabar_nap=0
sec.gnabar_nap=0.0015161014*dgnaf_proxF
sec.gkbar_kas=0.013754082
sec.gkbar_kaf=0.05
# sec.gkbar_kas=0
# sec.gkbar_kaf=0
sec.gkbar_kdr=0.0000228509
# sec.gkbar_kdr=0
sec.gkbar_bkkca=0.0000111911
sec.gkbar_skkca=0.01395996321
sec.pbar_caL=0.000001188
sec.pcaLbar_caL13=0.0000001017
sec.pbar_can=0.0000143303
sec.pcarbar_car=0.0000502025
sec.pcatbar_cat=0.0000007984
# sec.gkbar_bkkca=0.
# sec.gkbar_skkca=0
# sec.pbar_caL=0
# sec.pcaLbar_caL13=0
# sec.pbar_can=0
# sec.pcarbar_car=0
# sec.pcatbar_cat=0
for sec in self.mid:
# sec.gnabar_naf=round(0.890840924*dgnaf_midF,9)
sec.gnabar_naf=1.2738443502*dgnaf_midF
# sec.gnabar_naf=0
# sec.gnabar_nap=0
sec.gnabar_nap=0.0015161014*dgnaf_midF
sec.gkbar_kas=0.013754082*dgnaf_midF
sec.gkbar_kaf=0.05*dgnaf_midF
# sec.gkbar_kas=0
# sec.gkbar_kaf=0
sec.gkbar_kdr=0.0000228509
# sec.gkbar_kdr=0
sec.gkbar_bkkca=0.0000111911
sec.gkbar_skkca=0.01395996321
sec.pbar_caL=0.000001188
sec.pcaLbar_caL13=0.0000001017
sec.pbar_can=0.0000143303
sec.pcarbar_car=0.0000502025
sec.pcatbar_cat=0.0000007984
# sec.gkbar_bkkca=0
# sec.gkbar_skkca=0
# sec.pbar_caL=0
# sec.pcaLbar_caL13=0
# sec.pbar_can=0
# sec.pcarbar_car=0
# sec.pcatbar_cat=0
for sec in self.dist:
# sec.gnabar_naf=0.890840924*dgnaf_distF
sec.gnabar_naf=1.2738443502*dgnaf_distF
# sec.gnabar_naf=0
# sec.gnabar_nap=0
sec.gnabar_nap=0.0015161014*dgnaf_distF
sec.gkbar_kas=0.013754082*dgnaf_distF
sec.gkbar_kaf=0.05*dgnaf_distF
# sec.gkbar_kas=0
# sec.gkbar_kaf=0
sec.gkbar_kdr=0.0000228509
# sec.gkbar_kdr=0
sec.gkbar_bkkca=0.0000111911
sec.gkbar_skkca=0.01395996321
sec.pbar_caL=0.000001188
sec.pcaLbar_caL13=0.0000001017
sec.pbar_can=0.0000143303
sec.pcarbar_car=0.0000502025
sec.pcatbar_cat=0.0000007984
# sec.gkbar_bkkca=0.
# sec.gkbar_skkca=0
# sec.pbar_caL=0
# sec.pcaLbar_caL13=0
# sec.pbar_can=0
# sec.pcarbar_car=0
# sec.pcatbar_cat=0
for sec in self.axon:
sec.gnabar_naf=1.6655595931
sec.gkbar_kas=0.03380935
sec.gkbar_kaf=0.0339222128
sec.gnabar_nap=0.00059488416
sec.gkbar_kdr=0.0098251214
# sec.gnabar_naf=0
# sec.gkbar_kas=0
# sec.gkbar_kaf=0
# sec.gnabar_nap=0
# sec.gkbar_kdr=0