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cellClasses.py
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cellClasses.py
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from neuron import h
class modelcell():
def __init__(self):
self.x = 0; self.y = 0; self.z = 0
self.gid = -1
self.core_i=-1
self.coretype_i=-1
self.is_art = 0
self.nc = []
self.pre_list = []
class GranuleCell(modelcell):
""" Granule Cell definition """
def __init__(self, gid = -1):
super().__init__()
self.gid = gid
self.create_sections()
self.build_topology()
self.build_subsets() # subsets()
self.define_geometry() # geom()
self.define_biophysics() # biophys()
self.addSynapses() # synapses
def __repr__(self):
return "Pyramidal Cell {}".format(self.gid)
def create_sections(self):
self.soma = h.Section(name='soma', cell=self)
self.gcdend1 = []
self.gcdend2 = []
for r in range(4):
self.gcdend1.append(h.Section(name='gcdend1['+str(r)+']', cell=self))
self.gcdend2.append(h.Section(name='gcdend1['+str(r)+']', cell=self))
def build_topology(self):
self.gcdend1[0].connect(self.soma(1))
self.gcdend2[0].connect(self.soma(1))
for r in range(1,4):
self.gcdend1[r].connect(self.gcdend1[r-1](1))
self.gcdend2[r].connect(self.gcdend2[r-1](1))
def define_geometry(self):
soma {nseg=1 L=16.8 diam=16.8} // changed L & diam
gcdend1 [0] {nseg=1 L=50 diam=3}
for i = 1, 3 gcdend1 [i] {nseg=1 L=150 diam=3}
gcdend2 [0] {nseg=1 L=50 diam=3}
for i = 1, 3 gcdend2 [i] {nseg=1 L=150 diam=3}
self.soma.nseg = 1
self.soma.L = 16.8
self.soma.diam = 16.8
self.gcdend1[0].nseg = 1
self.gcdend1[0].L = 50
self.gcdend1[0].diam = 3
self.gcdend2[0].nseg = 1
self.gcdend2[0].L = 50
self.gcdend2[0].diam = 3
for r in range(1,4):
self.gcdend1[r].nseg = 1
self.gcdend1[r].L = 150
self.gcdend1[r].diam = 3
self.gcdend2[r].nseg = 1
self.gcdend2[r].L = 150
self.gcdend2[r].diam = 3
def build_subsets(self):
self.all = h.SectionList()
self.all.wholetree(sec=self.soma)
self.gcldend = h.SectionList()
self.gcldend.append(self.gcdend1[0])
self.gcldend.append(self.gcdend2[0])
self.pdend = h.SectionList()
self.pdend.append(self.gcdend1[1])
self.pdend.append(self.gcdend2[1])
self.mdend = h.SectionList()
self.mdend.append(self.gcdend1[2])
self.mdend.append(self.gcdend2[2])
self.ddend = h.SectionList()
self.ddend.append(self.gcdend1[3])
self.ddend.append(self.gcdend2[3])
def define_biophysics(self):
for sec in self.all:
sec.insert("ccanl")
sec.catau_ccanl = 10
sec.caiinf_ccanl = 5.e-6
sec.Ra = 210
self.soma.insert("ichan2") # modified from Aradi and Soltesz 2002
self.soma.insert("borgka") # KA from Aradi and Soltesz 2002
self.soma.insert("nca") # NVA Ca++-L type current
self.soma.insert("lca") # HVA Ca++-L type current
self.soma.insert("cat") # m-type potassium current
self.soma.insert("gskch") # SK channel from Aradi and Soltesz 2002
self.soma.insert("cagk") # from Migliore et al., 1995
for seg in self.soma:
seg.cm = 1
seg.gnatbar_ichan2=0.12
seg.gkfbar_ichan2=0.016
seg.gksbar_ichan2=0.006
seg.gl_ichan2=0.006
seg.gkabar_borgka=0.012
seg.gncabar_nca=0.002
seg.glcabar_lca=0.005
seg.gcatbar_cat=0.000037
seg.gskbar_gskch=0.001
seg.gkbar_cagk=0.0006
for sec in self.gcldend:
sec.insert("ichan2") # modified from Aradi and Soltesz 2002
sec.insert("nca") # NVA Ca++-L type current
sec.insert("lca") # HVA Ca++-L type current
sec.insert("cat") # m-type potassium current
sec.insert("gskch") # SK channel from Aradi and Soltesz 2002
sec.insert("cagk") # from Migliore et al., 1995
for seg in sec:
seg.cm = 1
seg.gnatbar_ichan2=0.018
seg.gkfbar_ichan2=0.004
seg.gksbar_ichan2=0.006
seg.gl_ichan2=0.00004
seg.gncabar_nca=0.003
seg.glcabar_lca=0.0075
seg.gcatbar_cat=0.000075
seg.gskbar_gskch=0.0004
seg.gkbar_cagk=0.0006
for sec in self.pdend:
sec.insert("ichan2") # modified from Aradi and Soltesz 2002
sec.insert("nca") # NVA Ca++-L type current
sec.insert("lca") # HVA Ca++-L type current
sec.insert("cat") # m-type potassium current
sec.insert("gskch") # SK channel from Aradi and Soltesz 2002
sec.insert("cagk") # from Migliore et al., 1995
for seg in sec:
seg.cm = 1.6
seg.gnatbar_ichan2=0.013
seg.gkfbar_ichan2=0.004
seg.gksbar_ichan2=0.006
seg.gl_ichan2=0.000063
seg.gncabar_nca=0.001
seg.glcabar_lca=0.0075
seg.gcatbar_cat=0.00025
seg.gskbar_gskch=0.0002
seg.gkbar_cagk=0.001
for sec in self.mdend:
sec.insert("ichan2") # modified from Aradi and Soltesz 2002
sec.insert("nca") # NVA Ca++-L type current
sec.insert("lca") # HVA Ca++-L type current
sec.insert("cat") # m-type potassium current
sec.insert("gskch") # SK channel from Aradi and Soltesz 2002
sec.insert("cagk") # from Migliore et al., 1995
for seg in sec:
seg.cm = 1.6
seg.gnatbar_ichan2=0.008
seg.gkfbar_ichan2=0.001
seg.gksbar_ichan2=0.006
seg.gl_ichan2=0.000063
seg.gncabar_nca=0.001
seg.glcabar_lca=0.0005
seg.gcatbar_cat=0.0005
seg.gskbar_gskch=0.0
seg.gkbar_cagk=0.0024
for sec in self.ddend:
sec.insert("ichan2") # modified from Aradi and Soltesz 2002
sec.insert("nca") # NVA Ca++-L type current
sec.insert("lca") # HVA Ca++-L type current
sec.insert("cat") # m-type potassium current
sec.insert("gskch") # SK channel from Aradi and Soltesz 2002
sec.insert("cagk") # from Migliore et al., 1995
for seg in sec:
seg.cm = 1.6
seg.gnatbar_ichan2=0.0
seg.gkfbar_ichan2=0.001
seg.gksbar_ichan2=0.008
seg.gl_ichan2=0.000063
seg.gncabar_nca=0.001
seg.glcabar_lca=0.00
seg.gcatbar_cat=0.001
seg.gskbar_gskch=0.0
seg.gkbar_cagk=0.0024
for sec in self.all:
sec.enat = 45
sec.ekf = -90
sec.eks = -90
sec.ek=-90
sec.elca=130
sec.etca=130
sec.esk=-90
sec.el_ichan2 =-70
sec.cao_ccanl=2
def connect2target(self,target, delay = 1, weight=0.04): # { localobj nc #$o1 target point process, optional $o2 returned NetCon
self.nc.append(h.NetCon(self.soma(0.5)._ref_v, target, sec=self.soma))
self.nc[-1].threshold = -10 # mV
self.nc[-1].delay = delay # ms
self.nc[-1].weight[0] = weight # NetCon weight is a vector
return self.nc[-1]
def addSynapses(self):
self.pre_list = []
# PP syn based on data from Greg Hollrigel and Kevin Staley
syn_ = h.Exp2Syn(self.gcdend1[3](0.5))
self.pre_list.append(syn_)
syn_.tau1 = 1.5
syn_.tau2 = 5.5
syn_.e = 0
# PPsyn based on Greg and Staley
syn_ = h.Exp2Syn(self.gcdend2[3](0.5))
self.pre_list.append(syn_)
syn_.tau1 = 1.5
syn_.tau2 = 5.5
syn_.e = 0
# MC syn *** Estimated
syn_ = h.Exp2Syn(self.gcdend1[1](0.5))
self.pre_list.append(syn_)
syn_.tau1 = 1.5
syn_.tau2 = 5.5
syn_.e = 0
# MC syn *** Estimated
syn_ = h.Exp2Syn(self.gcdend2[1](0.5))
self.pre_list.append(syn_)
syn_.tau1 = 1.5
syn_.tau2 = 5.5
syn_.e = 0
# HIPP syn based on Harney and Jones corrected for temp
syn_ = h.Exp2Syn(self.gcdend1[3](0.5))
self.pre_list.append(syn_)
syn_.tau1 = 0.5
syn_.tau2 = 6
syn_.e = -70
# HIPP syn based on Harney and Jones corrected for temp
syn_ = h.Exp2Syn(self.gcdend2[3](0.5))
self.pre_list.append(syn_)
syn_.tau1 = 0.5
syn_.tau2 = 6
syn_.e = -70
# BC syn syn based on Bartos
syn_ = h.Exp2Syn(self.soma(0.5))
self.pre_list.append(syn_)
syn_.tau1 = 0.26
syn_.tau2 = 5.5
syn_.e = -70
# NOTE: SPROUTED SYNAPSE based on Molnar and Nadler
syn_ = h.Exp2Syn(self.gcdend1[1](0.5))
self.pre_list.append(syn_)
syn_.tau1 = 1.5
syn_.tau2 = 5.5
syn_.e = 0
# NOTE: SPROUTED SYNAPSE based on Molnar and Nadler
syn_ = h.Exp2Syn(self.gcdend2[1](0.5))
self.pre_list.append(syn_)
syn_.tau1 = 1.5
syn_.tau2 = 5.5
syn_.e = 0
# Total of 7 synapses per GC 0,1 PP; 2,3 MC; 4,5 HIPP and 6 BC 7,8 Sprout
class BasketCell(modelcell):
""" Basket Cell definition """
def __init__(self, gid = -1):
super().__init__()
self.gid = gid
self.create_sections()
self.build_topology()
self.build_subsets() # subsets()
self.define_geometry() # geom()
self.define_biophysics() # biophys()
self.addSynapses() # synapses
def __repr__(self):
return "Basket Cell {}".format(self.gid)
def create_sections(self):
self.soma = h.Section(name='soma', cell=self)
self.bcdend1 = []
self.bcdend2 = []
self.bcdend3 = []
self.bcdend4 = []
for r in range(4):
self.bcdend1.append(h.Section(name='bcdend1['+str(r)+']', cell=self))
self.bcdend2.append(h.Section(name='bcdend2['+str(r)+']', cell=self))
self.bcdend3.append(h.Section(name='bcdend3['+str(r)+']', cell=self))
self.bcdend4.append(h.Section(name='bcdend4['+str(r)+']', cell=self))
def build_topology(self):
self.bcdend1[0].connect(self.soma(1))
self.bcdend2[0].connect(self.soma(1))
self.bcdend3[0].connect(self.soma(0))
self.bcdend4[0].connect(self.soma(0))
for r in range(1,4):
self.bcdend1[r].connect(self.bcdend1[r-1](1))
self.bcdend2[r].connect(self.bcdend2[r-1](1))
self.bcdend3[r].connect(self.bcdend3[r-1](1))
self.bcdend4[r].connect(self.bcdend4[r-1](1))
def define_geometry(self):
self.soma.nseg=1
self.soma.L=20
self.soma.diam=15
for r in range(4):
self.bcdend1[r].nseg=1
self.bcdend1[r].L=75
self.bcdend1[r].diam=4-r
self.bcdend2[r].nseg=1
self.bcdend2[r].L=75
self.bcdend2[r].diam=4-r
self.bcdend3[r].nseg=1
self.bcdend3[r].L=75
self.bcdend3[r].diam=4-r
self.bcdend4[r].nseg=1
self.bcdend4[r].L=75
self.bcdend4[r].diam=4-r
def build_subsets(self):
self.all = h.SectionList()
self.all.wholetree(sec=self.soma)
self.adend = h.SectionList()
self.adend.append(self.bcdend1[0])
self.adend.append(self.bcdend2[0])
self.adend.append(self.bcdend3[0])
self.adend.append(self.bcdend4[0])
self.bdend = h.SectionList()
self.bdend.append(self.bcdend1[1])
self.bdend.append(self.bcdend2[1])
self.bdend.append(self.bcdend3[1])
self.bdend.append(self.bcdend4[1])
self.cdend = h.SectionList()
self.cdend.append(self.bcdend1[2])
self.cdend.append(self.bcdend2[2])
self.cdend.append(self.bcdend3[2])
self.cdend.append(self.bcdend4[2])
self.ddend = h.SectionList()
self.ddend.append(self.bcdend1[3])
self.ddend.append(self.bcdend2[3])
self.ddend.append(self.bcdend3[3])
self.ddend.append(self.bcdend4[3])
def define_biophysics(self):
self.soma.insert("ichan2") # modified from Aradi and Soltesz 2002
self.soma.insert("borgka") # KA from Aradi and Soltesz 2002
self.soma.insert("nca") # NVA Ca++-L type current
self.soma.insert("lca") # HVA Ca++-L type current
self.soma.insert("cat") # m-type potassium current
self.soma.insert("gskch") # SK channel from Aradi and Soltesz 2002
self.soma.insert("cagk") # from Migliore et al., 1995
for seg in self.soma:
seg.cm = 1
seg.gnatbar_ichan2=0.12
seg.gkfbar_ichan2=0.016
seg.gksbar_ichan2=0.006
seg.gl_ichan2=0.006
seg.gkabar_borgka=0.012
seg.gncabar_nca=0.002
seg.glcabar_lca=0.005
seg.gcatbar_cat=0.000037
seg.gskbar_gskch=0.001
seg.gkbar_cagk=0.0006
for sec in self.gcldend:
sec.insert("ichan2") # modified from Aradi and Soltesz 2002
sec.insert("nca") # NVA Ca++-L type current
sec.insert("lca") # HVA Ca++-L type current
sec.insert("cat") # m-type potassium current
sec.insert("gskch") # SK channel from Aradi and Soltesz 2002
sec.insert("cagk") # from Migliore et al., 1995
for seg in sec:
seg.cm = 1
seg.gnatbar_ichan2=0.018
seg.gkfbar_ichan2=0.004
seg.gksbar_ichan2=0.006
seg.gl_ichan2=0.00004
seg.gncabar_nca=0.003
seg.glcabar_lca=0.0075
seg.gcatbar_cat=0.000075
seg.gskbar_gskch=0.0004
seg.gkbar_cagk=0.0006
for sec in self.pdend:
sec.insert("ichan2") # modified from Aradi and Soltesz 2002
sec.insert("nca") # NVA Ca++-L type current
sec.insert("lca") # HVA Ca++-L type current
sec.insert("cat") # m-type potassium current
sec.insert("gskch") # SK channel from Aradi and Soltesz 2002
sec.insert("cagk") # from Migliore et al., 1995
for seg in sec:
seg.cm = 1.6
seg.gnatbar_ichan2=0.013
seg.gkfbar_ichan2=0.004
seg.gksbar_ichan2=0.006
seg.gl_ichan2=0.000063
seg.gncabar_nca=0.001
seg.glcabar_lca=0.0075
seg.gcatbar_cat=0.00025
seg.gskbar_gskch=0.0002
seg.gkbar_cagk=0.001
for sec in self.mdend:
sec.insert("ichan2") # modified from Aradi and Soltesz 2002
sec.insert("nca") # NVA Ca++-L type current
sec.insert("lca") # HVA Ca++-L type current
sec.insert("cat") # m-type potassium current
sec.insert("gskch") # SK channel from Aradi and Soltesz 2002
sec.insert("cagk") # from Migliore et al., 1995
for seg in sec:
seg.cm = 1.6
seg.gnatbar_ichan2=0.008
seg.gkfbar_ichan2=0.001
seg.gksbar_ichan2=0.006
seg.gl_ichan2=0.000063
seg.gncabar_nca=0.001
seg.glcabar_lca=0.0005
seg.gcatbar_cat=0.0005
seg.gskbar_gskch=0.0
seg.gkbar_cagk=0.0024
for sec in self.ddend:
sec.insert("ichan2") # modified from Aradi and Soltesz 2002
sec.insert("nca") # NVA Ca++-L type current
sec.insert("lca") # HVA Ca++-L type current
sec.insert("cat") # m-type potassium current
sec.insert("gskch") # SK channel from Aradi and Soltesz 2002
sec.insert("cagk") # from Migliore et al., 1995
for seg in sec:
seg.cm = 1.6
seg.gnatbar_ichan2=0.0
seg.gkfbar_ichan2=0.001
seg.gksbar_ichan2=0.008
seg.gl_ichan2=0.000063
seg.gncabar_nca=0.001
seg.glcabar_lca=0.00
seg.gcatbar_cat=0.001
seg.gskbar_gskch=0.0
seg.gkbar_cagk=0.0024
for sec in self.all:
sec.enat = 55
sec.ekf = -90
sec.ek = -90
sec.esk=-90
sec.elca=130
sec.el_ichan2 =-60.06
sec.Ra = 100
sec.insert("ccanl")
sec.catau_ccanl = 10
sec.caiinf_ccanl = 5.e-6
sec.cao_ccanl=2
def connect2target(self,target, delay = 1, weight=0.04): # { localobj nc #$o1 target point process, optional $o2 returned NetCon
self.nc.append(h.NetCon(self.soma(0.5)._ref_v, target, sec=self.soma))
self.nc[-1].threshold = -10 # mV
self.nc[-1].delay = delay # ms
self.nc[-1].weight[0] = weight # NetCon weight is a vector
return self.nc[-1]
def addSynapses(self):
self.pre_list = []
# PP(AMPA) syn to apical dist dend Dingledine '95
syn_ = h.Exp2Syn(self.bcdend1[3](0.5))
self.pre_list.append(syn_)
syn_.tau1 = 2
syn_.tau2 = 6.3
syn_.e = 0
# PP(AMPA) syn to apical dist dend Dingledine '95
syn_ = h.Exp2Syn(self.bcdend2[3](0.5))
self.pre_list.append(syn_)
syn_.tau1 = 2
syn_.tau2 = 6.3
syn_.e = 0
# GC(AMPA) syn to prox dend Geiger '97
syn_ = h.Exp2Syn(self.bcdend1[0](0.5))
self.pre_list.append(syn_)
syn_.tau1 = .3
syn_.tau2 = .6
syn_.e = 0
# GC(AMPA) syn to prox dend Geiger '97
syn_ = h.Exp2Syn(self.bcdend2[0](0.5))
self.pre_list.append(syn_)
syn_.tau1 = .3
syn_.tau2 = .6
syn_.e = 0
# GC(AMPA) syn to prox dend Geiger '97
syn_ = h.Exp2Syn(self.bcdend3[0](0.5))
self.pre_list.append(syn_)
syn_.tau1 = .3
syn_.tau2 = .6
syn_.e = 0
# GC(AMPA) syn to prox dend Geiger '97
syn_ = h.Exp2Syn(self.bcdend4[0](0.5))
self.pre_list.append(syn_)
syn_.tau1 = .3
syn_.tau2 = .6
syn_.e = 0
# MC(AMPA) syn to apical IML dend
syn_ = h.Exp2Syn(self.bcdend1[1](0.5))
self.pre_list.append(syn_)
syn_.tau1 = 0.9
syn_.tau2 = 3.6
syn_.e = 0
# MC(AMPA) syn to apical IML dend
syn_ = h.Exp2Syn(self.bcdend2[1](0.5))
self.pre_list.append(syn_)
syn_.tau1 = 0.9
syn_.tau2 = 3.6
syn_.e = 0
# NOTE: BC(GABA) syn to apical IML dend Bartos
syn_ = h.Exp2Syn(self.bcdend1[1](0.5))
self.pre_list.append(syn_)
syn_.tau1 = 0.16
syn_.tau2 = 1.8
syn_.e = -70
# NOTE: BC(GABA) syn to apical IML dend Bartos
syn_ = h.Exp2Syn(self.bcdend2[1](0.5))
self.pre_list.append(syn_)
syn_.tau1 = 0.16
syn_.tau2 = 1.8
syn_.e = -70
# NOTE: HIPP(GABA) syn to apical distal dend
syn_ = h.Exp2Syn(self.bcdend1[3](0.5))
self.pre_list.append(syn_)
syn_.tau1 = 0.4
syn_.tau2 = 5.8
syn_.e = -70
# NOTE: HIPP(GABA) syn to apical distal dend
syn_ = h.Exp2Syn(self.bcdend2[3](0.5))
self.pre_list.append(syn_)
syn_.tau1 = 0.4
syn_.tau2 = 5.8
syn_.e = -70
# Total of 12 synapses 0,1 PP; 2-5 GC; 6,7 MC; 8,9 BC; 10,11 HIPP
class MossyCell(modelcell):
""" Mossy Cell definition """
def __init__(self, gid = -1):
super().__init__()
self.gid = gid
self.create_sections()
self.build_topology()
self.build_subsets() # subsets()
self.define_geometry() # geom()
self.define_biophysics() # biophys()
self.addSynapses() # synapses
def __repr__(self):
return "Mossy Cell {}".format(self.gid)
def create_sections(self):
self.soma = h.Section(name='soma', cell=self)
self.mcdend1 = []
self.mcdend2 = []
self.mcdend3 = []
self.mcdend4 = []
for r in range(4):
self.mcdend1.append(h.Section(name='mcdend1['+str(r)+']', cell=self))
self.mcdend2.append(h.Section(name='mcdend2['+str(r)+']', cell=self))
self.mcdend3.append(h.Section(name='mcdend3['+str(r)+']', cell=self))
self.mcdend4.append(h.Section(name='mcdend4['+str(r)+']', cell=self))
def build_topology(self):
self.mcdend1[0].connect(self.soma(1))
self.mcdend2[0].connect(self.soma(1))
self.mcdend3[0].connect(self.soma(0))
self.mcdend4[0].connect(self.soma(0))
for r in range(1,4):
self.mcdend1[r].connect(self.mcdend1[r-1](1))
self.mcdend2[r].connect(self.mcdend2[r-1](1))
self.mcdend3[r].connect(self.mcdend3[r-1](1))
self.mcdend4[r].connect(self.mcdend4[r-1](1))
def define_geometry(self):
self.soma.nseg=1
self.soma.L=20
self.soma.diam=20
diamlist=[5.78, 4, 2.5, 1]
for r in range(4):
self.mcdend1[r].nseg=1
self.mcdend1[r].L=50
self.mcdend1[r].diam=diamlist[r]
self.mcdend2[r].nseg=1
self.mcdend2[r].L=50
self.mcdend2[r].diam=diamlist[r]
self.mcdend3[r].nseg=1
self.mcdend3[r].L=50
self.mcdend3[r].diam=diamlist[r]
self.mcdend4[r].nseg=1
self.mcdend4[r].L=50
self.mcdend4[r].diam=diamlist[r]
def build_subsets(self):
self.all = h.SectionList()
self.all.wholetree(sec=self.soma)
self.pdend = h.SectionList()
self.pdend.append(self.mcdend1[0])
self.pdend.append(self.mcdend2[0])
self.pdend.append(self.mcdend3[0])
self.pdend.append(self.mcdend4[0])
self.ddend = h.SectionList()
for r in range(1,4):
self.ddend.append(self.mcdend1[r])
self.ddend.append(self.mcdend2[r])
self.ddend.append(self.mcdend3[r])
self.ddend.append(self.mcdend4[r])
def define_biophysics(self):
self.soma.insert("ichan2") # modified from Aradi and Soltesz 2002
self.soma.cm=0.6
for seg in self.soma:
seg.cm = 1
seg.gnatbar_ichan2=0.12
seg.gkfbar_ichan2=0.0005
seg.gl_ichan2=0.000011
for sec in self.pdend:
sec.insert("ichan2") # modified from Aradi and Soltesz 2002
for seg in sec:
seg.cm = 1
seg.gnatbar_ichan2=0.12
seg.gkfbar_ichan2=0.0005
seg.gl_ichan2=0.000044
sec.cm = 2.4
for sec in self.ddend:
sec.insert("ichan2") # modified from Aradi and Soltesz 2002
for seg in sec:
seg.cm = 1.6
seg.gnatbar_ichan2=0.0
seg.gkfbar_ichan2=0.00
seg.gl_ichan2=0.000044
sec.cm = 2.4
for sec in self.all:
sec.insert("borgka") # KA from Aradi and Soltesz 2002
sec.insert("nca") # NVA Ca++-L type current
sec.insert("lca") # HVA Ca++-L type current
sec.insert("gskch") # SK channel from Aradi and Soltesz 2002
sec.insert("cagk") # from Migliore et al., 1995
sec.insert("hyperde3") # from Migliore et al., 1995
sec.insert("ccanl")
for seg in sec:
seg.gkabar_borgka=0.00001
seg.gncabar_nca=0.00008
seg.glcabar_lca=0.0006
seg.gskbar_gskch=0.016
seg.gkbar_cagk=0.0165
seg.ghyfbar_hyperde3=0.000005
seg.ghysbar_hyperde3=0.000005
sec.catau_ccanl = 10
sec.caiinf_ccanl = 5.e-6
sec.enat = 55
sec.ekf = -90
sec.ek = -90
sec.esk=-90
sec.elca=130
sec.el_ichan2 =-70.45
sec.ehyf=-40
sec.ehys=-40
sec.Ra = 100
self.cao_ccanl=2
def connect2target(self,target, delay = 1, weight=0.04): # { localobj nc #$o1 target point process, optional $o2 returned NetCon
self.nc.append(h.NetCon(self.soma(0.5)._ref_v, target, sec=self.soma))
self.nc[-1].threshold = -10 # mV
self.nc[-1].delay = delay # ms
self.nc[-1].weight[0] = weight # NetCon weight is a vector
return self.nc[-1]
def addSynapses(self):
self.pre_list = []
# PP(AMPA) syn to dist dend similar to PP to GC
syn_ = h.Exp2Syn(self.mcdend1[3](0.7))
self.pre_list.append(syn_)
syn_.tau1 = 1.5
syn_.tau2 = 5.5
syn_.e = 0
# PP(AMPA) syn to dist dend similar to PP to GC
syn_ = h.Exp2Syn(self.mcdend2[3](0.7))
self.pre_list.append(syn_)
syn_.tau1 = 1.5
syn_.tau2 = 5.5
syn_.e = 0
# PP(AMPA) syn to dist dend similar to PP to GC
syn_ = h.Exp2Syn(self.mcdend3[3](0.7))
self.pre_list.append(syn_)
syn_.tau1 = 1.5
syn_.tau2 = 5.5
syn_.e = 0
# PP(AMPA) syn to dist dend similar to PP to GC
syn_ = h.Exp2Syn(self.mcdend4[3](0.7))
self.pre_list.append(syn_)
syn_.tau1 = 1.5
syn_.tau2 = 5.5
syn_.e = 0
# GC(AMPA) syn to prox dend similar to GC>CA3 Jonas '93
syn_ = h.Exp2Syn(self.mcdend1[0](0.5))
self.pre_list.append(syn_)
syn_.tau1 = .5
syn_.tau2 = 6.2
syn_.e = 0
# GC(AMPA) syn to prox dend similar to GC>CA3 Jonas '93
syn_ = h.Exp2Syn(self.mcdend2[0](0.5))
self.pre_list.append(syn_)
syn_.tau1 = .5
syn_.tau2 = 6.2
syn_.e = 0
# GC(AMPA) syn to prox dend similar to GC>CA3 Jonas '93
syn_ = h.Exp2Syn(self.mcdend3[0](0.5))
self.pre_list.append(syn_)
syn_.tau1 = .5
syn_.tau2 = 6.2
syn_.e = 0
# GC(AMPA) syn to prox dend similar to GC>CA3 Jonas '93
syn_ = h.Exp2Syn(self.mcdend4[0](0.5))
self.pre_list.append(syn_)
syn_.tau1 = .5
syn_.tau2 = 6.2
syn_.e = 0
# MC(AMPA) syn to prox dend similar to CA#>CA3 Aaron
syn_ = h.Exp2Syn(self.mcdend1[0](0.5))
self.pre_list.append(syn_)
syn_.tau1 = 0.45
syn_.tau2 = 2.2
syn_.e = 0
# MC(AMPA) syn to prox dend similar to CA#>CA3 Aaron
syn_ = h.Exp2Syn(self.mcdend2[0](0.5))
self.pre_list.append(syn_)
syn_.tau1 = 0.45
syn_.tau2 = 2.2
syn_.e = 0
# MC(AMPA) syn to prox dend similar to CA#>CA3 Aaron
syn_ = h.Exp2Syn(self.mcdend3[0](0.5))
self.pre_list.append(syn_)
syn_.tau1 = 0.45
syn_.tau2 = 2.2
syn_.e = 0
# MC(AMPA) syn to prox dend similar to CA#>CA3 Aaron
syn_ = h.Exp2Syn(self.mcdend4[0](0.5))
self.pre_list.append(syn_)
syn_.tau1 = 0.45
syn_.tau2 = 2.2
syn_.e = 0
# BC(GABA) syn to prox dend based on BC>CA3 Bartos PNAS (mice)
syn_ = h.Exp2Syn(self.soma(0.5))
self.pre_list.append(syn_)
syn_.tau1 = 0.3
syn_.tau2 = 3.3
syn_.e = -70
# HIPP(GABA) syn to prox dend based on Hilar>GC Harney&Jones
syn_ = h.Exp2Syn(self.mcdend1[2](0.5))
self.pre_list.append(syn_)
syn_.tau1 = 0.5
syn_.tau2 = 6
syn_.e = -70
# HIPP(GABA) syn to prox dend based on Hilar>GC Harney&Jones
syn_ = h.Exp2Syn(self.mcdend2[2](0.5))
self.pre_list.append(syn_)
syn_.tau1 = 0.5
syn_.tau2 = 6
syn_.e = -70
# HIPP(GABA) syn to prox dend based on Hilar>GC Harney&Jones
syn_ = h.Exp2Syn(self.mcdend3[2](0.5))
self.pre_list.append(syn_)
syn_.tau1 = 0.5
syn_.tau2 = 6
syn_.e = -70
# HIPP(GABA) syn to prox dend based on Hilar>GC Harney&Jones
syn_ = h.Exp2Syn(self.mcdend4[2](0.5))
self.pre_list.append(syn_)
syn_.tau1 = 0.5
syn_.tau2 = 6
syn_.e = -70
# Total of 17 synapses 0-3 PP; 4-7 GC; 8-11 MC; 12 BC; 13-16 HIPP
class HIPPCell(modelcell):
""" HIPP Cell definition """
def __init__(self, gid = -1):
super().__init__()
self.gid = gid
self.create_sections()
self.build_topology()
self.build_subsets() # subsets()
self.define_geometry() # geom()
self.define_biophysics() # biophys()
self.addSynapses() # synapses
def __repr__(self):
return "HIPP Cell {}".format(self.gid)
def create_sections(self):
self.soma = h.Section(name='soma', cell=self)
self.hcdend1 = []
self.hcdend2 = []
self.hcdend3 = []
self.hcdend4 = []
for r in range(3):
self.hcdend1.append(h.Section(name='hcdend1['+str(r)+']', cell=self))
self.hcdend2.append(h.Section(name='hcdend2['+str(r)+']', cell=self))
self.hcdend3.append(h.Section(name='hcdend3['+str(r)+']', cell=self))
self.hcdend4.append(h.Section(name='hcdend4['+str(r)+']', cell=self))
def build_topology(self):
self.hcdend1[0].connect(self.soma(1))
self.hcdend2[0].connect(self.soma(1))
self.hcdend3[0].connect(self.soma(0))
self.hcdend4[0].connect(self.soma(0))
for r in range(1,3):
self.hcdend1[r].connect(self.hcdend1[r-1](1))
self.hcdend2[r].connect(self.hcdend2[r-1](1))
self.hcdend3[r].connect(self.hcdend3[r-1](1))
self.hcdend4[r].connect(self.hcdend4[r-1](1))
def define_geometry(self):
self.soma.nseg=1
self.soma.L=20
self.soma.diam=10
diamlist=[5.78, 4, 2.5, 1]
for r in range(3):
self.mcdend1[r].nseg=1
self.hcdend1[r].L=75
self.hcdend1[r].diam=3-r
self.hcdend2[r].nseg=1
self.hcdend2[r].L=75
self.hcdend2[r].diam=3-r
self.hcdend3[r].nseg=1
self.hcdend3[r].L=50
self.hcdend3[r].diam=3-r
self.hcdend4[r].nseg=1
self.hcdend4[r].L=50
self.hcdend4[r].diam=3-r
def build_subsets(self):
self.all = h.SectionList()
self.all.wholetree(sec=self.soma)
self.pdend = h.SectionList()
self.pdend.append(self.hcdend1[0])
self.pdend.append(self.hcdend2[0])
self.pdend.append(self.hcdend3[0])
self.pdend.append(self.hcdend4[0])
self.ddend = h.SectionList()
for r in range(1,3):
self.ddend.append(self.hcdend1[r])
self.ddend.append(self.hcdend2[r])
self.ddend.append(self.hcdend3[r])
self.ddend.append(self.hcdend4[r])
def define_biophysics(self):
self.soma.insert("ichan2") # modified from Aradi and Soltesz 2002
self.soma.cm=0.6
for seg in self.soma:
seg.gnatbar_ichan2=0.2
seg.gkfbar_ichan2=0.006
seg.gl_ichan2=0.000036
self.soma.cm=1.1
for sec in self.pdend:
sec.insert("ichan2") # modified from Aradi and Soltesz 2002
for seg in sec:
seg.gnatbar_ichan2=0.2
seg.gkfbar_ichan2=0.006
seg.gl_ichan2=0.000036
sec.cm = 1.1
for sec in self.ddend:
sec.insert("ichan2") # modified from Aradi and Soltesz 2002
for seg in sec:
seg.gnatbar_ichan2=0.0
seg.gkfbar_ichan2=0.00
seg.gl_ichan2=0.000036
sec.cm = 1.1
for sec in self.all:
sec.insert("borgka") # KA from Aradi and Soltesz 2002
sec.insert("nca") # NVA Ca++-L type current