def make_NMDA( name ):
if moose.exists( '/library/' + name ):
return
NMDA = moose.NMDAChan( '/library/' + name )
NMDA.Ek = 0.0
NMDA.tau1 = 20.0e-3
NMDA.tau2 = 20.0e-3
NMDA.Gbar = 5 * SOMA_A
NMDA.CMg = 1.2 # [Mg]ext in mM
NMDA.KMg_A = 1.0/0.28
NMDA.KMg_B = 1.0/62
NMDA.temperature = 300 # Temperature in Kelvin.
NMDA.extCa = 1.5 # [Ca]ext in mM
NMDA.intCa = 0.00008 # [Ca]int in mM
NMDA.intCaScale = 1 # Scale factor from elec Ca units to mM
NMDA.intCaOffset = 0.00008 # Basal [Ca]int in mM
NMDA.condFraction = 0.02 # Fraction of conductance due to Ca
addmsg1 = moose.Mstring( NMDA.path + '/addmsg1' )
addmsg1.value = '. ICaOut ../Ca_conc current'
addmsg2 = moose.Mstring( NMDA.path + '/addmsg2' )
addmsg2.value = '../Ca_conc concOut . assignIntCa'
sh = moose.SimpleSynHandler( NMDA.path + '/sh' )
moose.connect( sh, 'activationOut', NMDA, 'activation' )
sh.numSynapses = 1
sh.synapse[0].weight = 1
return NMDA
def make_NMDA():
if moose.exists('NMDA'):
return
NMDA = moose.SynChan('NMDA')
NMDA.Ek = 0.0
NMDA.tau1 = 20.0e-3
NMDA.tau2 = 20.0e-3
NMDA.Gbar = 5 * SOMA_A
block = moose.MgBlock('/library/NMDA/block')
block.CMg = 1.2 # [Mg] in mM
block.Zk = 2
block.KMg_A = 1.0 / 0.28
block.KMg_B = 1.0 / 62
moose.connect(NMDA, 'channelOut', block, 'origChannel', 'OneToOne')
addmsg1 = moose.Mstring('/library/NMDA/addmsg1')
addmsg1.value = '.. channel ./block channel'
#Here we want to also tell the cell reader to _remove_ the original
#Gk, Ek term going from the channel to the compartment, as this is
# now handled by the MgBlock.
#addmsg2 = moose.Mstring( 'NMDA/addmsg2'
#addmsg2.value = 'DropMsg .. channel'
addmsg3 = moose.Mstring('/library/NMDA/addmsg3')
addmsg3.value = '.. VmOut . Vm'
def make_NMDA():
if moose.exists('NMDA'):
return
NMDA = moose.SynChan('NMDA')
NMDA.Ek = 0.0
NMDA.tau1 = 20.0e-3
NMDA.tau2 = 20.0e-3
NMDA.Gbar = 5 * SOMA_A
block = moose.MgBlock('/library/NMDA/block')
block.CMg = 1.2 # [Mg] in mM
block.Zk = 2
block.KMg_A = 1.0 / 0.28
block.KMg_B = 1.0 / 62
moose.connect(NMDA, 'channelOut', block, 'origChannel', 'OneToOne')
addmsg1 = moose.Mstring('/library/NMDA/addmsg1')
addmsg1.value = '.. channel ./block channel'
#Here we want to also tell the cell reader to _remove_ the original
#Gk, Ek term going from the channel to the compartment, as this is
# now handled by the MgBlock.
#addmsg2 = moose.Mstring( 'NMDA/addmsg2'
#addmsg2.value = 'DropMsg .. channel'
addmsg1 = moose.Mstring('/library/NMDA/addmsg1')
addmsg1.value = '.. VmOut ./block Vm'
addmsg2 = moose.Mstring('/library/NMDA/addmsg2')
addmsg2.value = './block IkOut ../Ca_conc current'
addmsg3 = moose.Mstring('/library/NMDA/addmsg3')
addmsg3.value = '.. VmOut . Vm'
sh = moose.SimpleSynHandler('NMDA/sh')
moose.connect(sh, 'activationOut', NMDA, 'activation')
sh.numSynapses = 1
sh.synapse[0].weight = 1
def make_Ca( name ):
if moose.exists( '/library/' + name):
return
Ca = moose.HHChannel( '/library/' + name )
Ca.Ek = ECA
Ca.Gbar = 40 * SOMA_A
Ca.Gk = 0
Ca.Xpower = 2
Ca.Ypower = 1
Ca.Zpower = 0
xgate = moose.element( Ca.path + '/gateX' )
xA = np.array( [ 1.6e3, 0, 1.0, -1.0 * (0.065 + EREST_ACT), -0.01389, -20e3 * (0.0511 + EREST_ACT), 20e3, -1.0, -1.0 * (0.0511 + EREST_ACT), 5.0e-3, 3000, -0.1, 0.05 ] )
# xgate.min = -0.1
# xgate.max = 0.05
# xgate.divs = 3000
#// Converting Traub's expressions for the gCa/s alpha and beta functions
#// to SI units and entering the A, B, C, D and F parameters, we get:
# xgate.alpha( 1.6e3, 0, 1.0, -1.0 * (0.065 + EREST_ACT), -0.01389 )
# xgate.beta( -20e3 * (0.0511 + EREST_ACT), 20e3, -1.0, -1.0 * (0.0511 + EREST_ACT), 5.0e-3 )
#xgate.setupAlpha( xA )
xgate.alphaParms = xA
# The Y gate (gCa/r) is not quite of this form. For V > EREST_ACT, alpha =
# 5*{exp({-50*(V - EREST_ACT)})}. Otherwise, alpha = 5. Over the entire
# range, alpha + beta = 5. To create the Y_A and Y_B tables, we use some
# of the pieces of the setupalpha function.
ygate = moose.element( Ca.path + '/gateY' )
ygate.min = -0.1
ygate.max = 0.05
ygate.divs = 3000
yA = np.zeros( (ygate.divs + 1), dtype=float)
yB = np.zeros( (ygate.divs + 1), dtype=float)
#Fill the Y_A table with alpha values and the Y_B table with (alpha+beta)
dx = (ygate.max - ygate.min)/ygate.divs
x = ygate.min
for i in range( ygate.divs + 1 ):
if ( x > EREST_ACT):
yA[i] = 5.0 * math.exp( -50 * (x - EREST_ACT) )
else:
yA[i] = 0.0
#yB[i] = 6.0 - yA[i]
yB[i] = 5.0
x += dx
ygate.tableA = yA
ygate.tableB = yB
# Tell the cell reader that the current from this channel must be fed into
# the Ca_conc pool of calcium.
addmsg1 = moose.Mstring( Ca.path + '/addmsg1' )
addmsg1.value = '. IkOut ../Ca_conc current'
# in some compartments, whe have an NMDA_Ca_conc object to put the current
# into.
addmsg2 = moose.Mstring( Ca.path + '/addmsg2' )
addmsg2.value = '. IkOut ../NMDA_Ca_conc current'
# Here we put in an addmsg command for nernst objects, if any.
addmsg3 = moose.Mstring( Ca.path + '/addmsg3' )
addmsg3.value = '../Ca_conc/nernst Eout . setEk'
def CaN_SChan(name):
CaN_S = moose.HHChannel('/library/' + name)
CaN_S.Ek = ECa
CaN_S.Gbar = 300.0 * SOMA_A
CaN_S.Gk = 0.0
CaN_S.Xpower = 2.0
CaN_S.Ypower = 1.0
CaN_S.Zpower = 1.0
CaN_S.useConcentration = 1
CaN_S.instant = 4
celsius = 34
ki = .001
cai = 50e-6
cao = 10
mtfactor = 1.495491
htfactor = 1.760253
vhalfm = 23.916356
vhalfh = 39.676957
alph = 1.6e-4 * np.exp(-v * 1e3 / 48.4)
beth = 1 / (np.exp((-v * 1e3 + vhalfh) / 10.) + 1.)
alpm = 0.1967 * (-1.0 * v * 1e3 + vhalfm) / (np.exp(
(-1.0 * v * 1e3 + vhalfm) / 10.0) - 1.0)
betm = 0.046 * np.exp(-v * 1e3 / 20.73)
a = alpm
taum = mtfactor * 1 / (a + betm) * 1e-3
minf = a * mtfactor * 1 / (a + betm)
a = alph
tauh = htfactor * 1 / (a + beth) * 1e-3
hinf = a * htfactor * 1 / (a + beth)
xgate = moose.element(CaN_S.path + '/gateX')
xgate.min = Vmin
xgate.max = Vmax
xgate.divs = Vdivs
xgate.tableA = minf / taum
xgate.tableB = 1.0 / taum
ygate = moose.element(CaN_S.path + '/gateY')
ygate.min = Vmin
ygate.max = Vmax
ygate.divs = Vdivs
ygate.tableA = hinf / tauh
ygate.tableB = 1.0 / tauh
zgate = moose.element(CaN_S.path + '/gateZ')
zgate.min = Camin
zgate.max = Camax
zgate.divs = Cadivs
zgate.tableA = ki / (ki + ca)
zgate.tableB = ki / (ki + ca)
addmsg2 = moose.Mstring(CaN_S.path + '/addmsg2')
addmsg2.value = '. IkOut ../Ca_conc current'
addmsg4 = moose.Mstring(CaN_S.path + '/addmsg4')
addmsg4.value = '../Ca_conc concOut . concen'
return CaN_S
def __new__(cls, name, bases, cdict):
global prototypes
# classes that set absract=True will be
# abstract classes. Others will have the prototype insatntiated.
if 'abstract' in cdict and cdict['abstract'] == True:
return type.__new__(cls, name, bases, cdict)
proto = moose.HHChannel('%s/%s' % (config.library.path, name))
xpower = get_class_field(name, cdict, bases, 'Xpower', default=0.0)
if xpower > 0:
proto.Xpower = xpower
gate = moose.HHGate('%s/gateX' % (proto.path))
setup_gate_tables(gate, cdict, bases)
cdict['xGate'] = gate
ypower = get_class_field(name, cdict, bases, 'Ypower', default=0.0)
if ypower > 0:
proto.Ypower = ypower
gate = moose.HHGate('%s/gateY' % (proto.path))
setup_gate_tables(gate, cdict, bases)
cdict['yGate'] = gate
zpower = get_class_field(name, cdict, bases, 'Zpower', default=0.0)
if zpower > 0:
proto.Zpower = zpower
gate = moose.HHGate('%s/gateZ' % (proto.path))
setup_gate_tables(gate, cdict, bases)
cdict['zGate'] = gate
ca_msg_field = moose.Mstring('%s/addmsg1' % (proto.path))
ca_msg_field.value = '../CaPool concOut . concen'
proto.instant = get_class_field(name,
cdict,
bases,
'instant',
default=0)
proto.useConcentration = True
proto.Ek = get_class_field(name, cdict, bases, 'Ek', default=0.0)
X = get_class_field(name, cdict, bases, 'X')
if X is not None:
proto.X = X
Y = get_class_field(name, cdict, bases, 'Y')
if Y is not None:
proto.Y = Y
Z = get_class_field(name, cdict, bases, 'Z')
if Z is not None:
proto.Z = Z
mstring_field = get_class_field(name, cdict, bases, 'mstring')
if mstring_field is not None:
# print 'mstring_field:', mstring_field
mstring = moose.Mstring('%s/%s' % (proto.path, mstring_field[0]))
mstring.value = mstring_field[1]
if 'annotation' in cdict:
info = moose.Annotator('%s/info' % (proto.path))
info.notes = '\n'.join('%s: %s' % kv
for kv in list(cdict['annotation'].items()))
# print proto.path, info.notes
cdict['prototype'] = proto
prototypes[name] = proto
config.logger.info('Created prototype: %s of class %s' %
(proto.path, name))
return type.__new__(cls, name, bases, cdict)
def Ca_N_Chan(name):
Ca_N = moose.HHChannel('/library/' + name)
Ca_N.Ek = ECa
Ca_N.Gbar = 300.0 * SOMA_A
Ca_N.Gk = 0.0
Ca_N.Xpower = 2.0
Ca_N.Ypower = 1.0
Ca_N.Zpower = 1.0
Ca_N.useConcentration = 1
Ca_N.instant = 4
ki = .001
cai = 50e-6
cao = 10
mtfactor = 1
htfactor = 1
vhalfm = 19.88
vhalfh = 39.0
alph = 1.6e-4 * np.exp(-v * 1e3 / 48.4)
beth = 1 / (np.exp((-v * 1e3 + vhalfh) / 10.) + 1.)
alpm = 0.1967 * (-1.0 * v * 1e3 + vhalfm) / (np.exp(
(-1.0 * v * 1e3 + vhalfm) / 10.0) - 1.0)
betm = 0.046 * np.exp(-v * 1e3 / 20.73)
a = alpm
taum = mtfactor * 1 / (a + betm)
minf = a * mtfactor * 1 / (a + betm)
a = alph
tauh = htfactor * 1 / (a + beth)
hinf = a * htfactor * 1 / (a + beth)
xgate = moose.element(Ca_N.path + '/gateX')
xgate.min = Vmin
xgate.max = Vmax
xgate.divs = Vdivs
xgate.tableA = minf / taum * 1e3
xgate.tableB = 1.0 / taum * 1e3
ygate = moose.element(Ca_N.path + '/gateY')
ygate.min = Vmin
ygate.max = Vmax
ygate.divs = Vdivs
ygate.tableA = hinf / tauh * 1e3
ygate.tableB = 1.0 / tauh * 1e3
zgate = moose.element(Ca_N.path + '/gateZ')
zgate.min = Camin
zgate.max = Camax
zgate.divs = Cadivs
zgate.tableA = ki / (ki + ca)
zgate.tableB = ki / (ki + ca)
addmsg2 = moose.Mstring(Ca_N.path + '/addmsg2')
addmsg2.value = '. IkOut ../Ca_conc current'
addmsg4 = moose.Mstring(Ca_N.path + '/addmsg4')
addmsg4.value = '../Ca_conc concOut . concen'
return Ca_N
def readSynapseML(self, synapseElement, units="SI units"):
if 'Physiological Units' in units: # see pg 219 (sec 13.2) of Book of Genesis
Vfactor = 1e-3 # V from mV
Tfactor = 1e-3 # s from ms
Gfactor = 1e-3 # S from mS
elif 'SI Units' in units:
Vfactor = 1.0
Tfactor = 1.0
Gfactor = 1.0
else:
pu.fatal("Wrong units %s exiting ..." % units)
sys.exit(1)
if not moose.exists('/library'):
moose.Neutral('/library')
synname = synapseElement.attrib['name']
if utils.neuroml_debug:
pu.info("Loading synapse : %s into /library" % synname)
moosesynapse = moose.SynChan('/library/' + synname)
doub_exp_syn = synapseElement.find('./{' + self.cml + '}doub_exp_syn')
moosesynapse.Ek = float(
doub_exp_syn.attrib['reversal_potential']) * Vfactor
moosesynapse.Gbar = float(
doub_exp_syn.attrib['max_conductance']) * Gfactor
moosesynapse.tau1 = float(
doub_exp_syn.attrib['rise_time']) * Tfactor # seconds
moosesynapse.tau2 = float(
doub_exp_syn.attrib['decay_time']) * Tfactor # seconds
## The delay and weight can be set only after connecting a spike event generator.
## delay and weight are arrays: multiple event messages can be connected to a single synapse
## graded synapses are not supported by neuroml, so set to False here,
## see my Demo/neuroml/lobster_pyloric/STG_net.py for how to still have graded synapses
moosesynapse_graded = moose.Mstring(moosesynapse.path + '/graded')
moosesynapse_graded.value = 'False'
moosesynapse_mgblock = moose.Mstring(moosesynapse.path + '/mgblockStr')
moosesynapse_mgblock.value = 'False'
## check if STDP synapse is present or not
stdp_syn = synapseElement.find('./{' + self.cml + '}stdp_syn')
if stdp_syn is None:
moosesynhandler = moose.SimpleSynHandler('/library/' + synname +
'/handler')
else:
moosesynhandler = moose.STDPSynHandler('/library/' + synname +
'/handler')
moosesynhandler.aPlus0 = float(stdp_syn.attrib['del_weight_ltp'])
moosesynhandler.aMinus0 = float(stdp_syn.attrib['del_weight_ltd'])
moosesynhandler.tauPlus = float(stdp_syn.attrib['tau_ltp'])
moosesynhandler.tauMinus = float(stdp_syn.attrib['tau_ltd'])
moosesynhandler.weightMax = float(
stdp_syn.attrib['max_syn_weight'])
moosesynhandler.weightMin = 0.0
## connect the SimpleSynHandler or the STDPSynHandler to the SynChan (double exp)
moose.connect(moosesynhandler, 'activationOut', moosesynapse,
'activation')
def KahpChanKO(name):
Kahp = moose.HHChannel('/library/' + name)
Kahp.Ek = Ek_K
Kahp.Gbar = 8.0 * SOMA_A
Kahp.Gk = 0.0
Kahp.Xpower = 0.0
Kahp.Ypower = 0.0
Kahp.Zpower = 1.0
Kahp.useConcentration = 1 #changed from Kahp.useConcentration = 0
zgate = moose.element(Kahp.path + '/gateZ')
zgate.min = Camin
zgate.max = Camax
zgate.divs = Cadivs
zA = np.zeros((zgate.divs + 1), dtype=float)
zB = np.zeros((zgate.divs + 1), dtype=float)
dx = (zgate.max - zgate.min) / zgate.divs
x = zgate.min
for i in range(zgate.divs + 1):
# zA[i] = min( 500.00 * x * Ca_scale, 10 ) #in paper, its zA[i] = min( 0.02 * x, 10 )
zA[i] = min(
0.02 * x / 2, 10
) #changed from zA[i] = min( 250.00 * x, 10 ) #2 times decrease in sensitivity
# zA[i] = min( 0.02 * x, 10.0 )
zB[i] = 1.0 + min(0.02 * x, 10) #changed from zB[i] = 1.0
x = x + dx
zgate.tableA = zA
zgate.tableB = zB
addmsg1 = moose.Mstring(Kahp.path + '/addmsg1')
addmsg1.value = '../Ca_conc concOut . concen'
return Kahp
def CaR_SChan(name):
CaR_S = moose.HHChannel('/library/' + name)
CaR_S.Ek = ECa
CaR_S.Gbar = 300.0 * SOMA_A
CaR_S.Gk = 0.0
CaR_S.Xpower = 3.0
CaR_S.Ypower = 1.0
CaR_S.Zpower = 0.0
celsius = 34
v = np.arange(Vmin, Vmax + dV, dV)
infm = 1.0 / (1 + np.exp((v + 60e-3) / (-3e-3)))
taum = 100e-3 + 0 * v
infh = 1.0 / (1 + np.exp((v + 62e-3) / (1e-3)))
tauh = 5e-3 + 0 * v
xgate = moose.element(CaR_S.path + '/gateX')
xgate.min = Vmin
xgate.max = Vmax
xgate.divs = Vdivs
xgate.tableA = infm / taum
xgate.tableB = 1.0 / taum
ygate = moose.element(CaR_S.path + '/gateY')
ygate.min = Vmin
ygate.max = Vmax
ygate.divs = Vdivs
ygate.tableA = infh / tauh
ygate.tableB = 1.0 / tauh
addmsg1 = moose.Mstring(CaR_S.path + '/addmsg1')
addmsg1.value = '. IkOut ../Ca_conc current'
return CaR_S
def KsAHP_Chan(name):
KsAHP = moose.HHChannel('/library/' + name)
KsAHP.Ek = EK
KsAHP.Gbar = 300.0 * SOMA_A
KsAHP.Gk = 0.0
KsAHP.Xpower = 0.0
KsAHP.Ypower = 0.0
KsAHP.Zpower = 3.0
KsAHP.useConcentration = 1
celsius = 36
gbar = 0.01
beta = 0.03e3
cac = 0.025
taumin = 0.5e-3
tadj = 3**((celsius - 22.0) / 10)
ca = np.arange(Camin, Camax + dCa, dCa)
car = (ca / cac)**2
m_inf = car / (1 + car)
tau_m = 1 / beta / (1 + car) / tadj
tau_m[tau_m < taumin] = taumin
zgate = moose.element(KsAHP.path + '/gateZ')
zgate.min = Camin
zgate.max = Camax
zgate.divs = Cadivs
zgate.tableA = m_inf / tau_m
zgate.tableB = 1.0 / tau_m
addmsg3 = moose.Mstring(KsAHP.path + '/addmsg3')
addmsg3.value = '../Ca_conc concOut . concen'
return KsAHP
def CaR_SChan(name): # Magee and Johnston (1995) and Poirazi et al. (2003) #Currently from Poirazi2003
CaR_S = moose.HHChannel( '/library/' + name )
CaR_S.Ek = ECa
CaR_S.Gbar = 300.0*SOMA_A
CaR_S.Gk = 0.0
CaR_S.Xpower = 3.0
CaR_S.Ypower = 1.0
CaR_S.Zpower = 0.0
celsius = 34
infm = 1 / (1 + np.exp((v*1e3+60)/(-3)))
taum = (100 + 0*v)*1e-3
infh = 1/ (1 + np.exp((v*1e3+62)/(1)))
tauh = (5 + 0*v)*1e-3
xgate = moose.element( CaR_S.path + '/gateX' )
xgate.min = Vmin
xgate.max = Vmax
xgate.divs = Vdivs
xgate.tableA = infm/taum
xgate.tableB = 1.0/taum
ygate = moose.element( CaR_S.path + '/gateY' )
ygate.min = Vmin
ygate.max = Vmax
ygate.divs = Vdivs
ygate.tableA = infh/tauh
ygate.tableB = 1.0/tauh
addmsg1 = moose.Mstring( CaR_S.path + '/addmsg1' )
addmsg1.value = '. IkOut ../Ca_conc current'
return CaR_S
def CaT_Chan(name):
CaT = moose.HHChannel('/library/' + name)
CaT.Ek = ECa
CaT.Gbar = 300.0 * SOMA_A
CaT.Gk = 0.0
CaT.Xpower = 2.0
CaT.Ypower = 1.0
CaT.Zpower = 1.0
CaT.useConcentration = 1
CaT.instant = 4
tBase = 23.5
celsius = 22
gcatbar = 0
ki = 0.001
cai = 5.e-5
cao = 2
tfa = 1
tfi = 0.68
v = np.arange(Vmin, Vmax + dV, dV)
alph = 1.6e-1 * np.exp(-(v + 57e-3) / 19e-3)
beth = 1e3 / (np.exp((-v + 15e-3) / 10e-3) + 1.0)
alpm = 0.1967e6 * (-1.0 * v + 19.88e-3) / (np.exp(
(-1.0 * v + 19.88e-3) / 10.0e-3) - 1.0)
betm = 0.046e3 * np.exp(-v / 22.73e-3)
a = alpm
taum = 1.0 / (tfa * (a + betm))
minf = a / (a + betm)
a = alph
tauh = 1.0 / (tfi * (a + beth))
hinf = a / (a + beth)
xgate = moose.element(CaT.path + '/gateX')
xgate.min = Vmin
xgate.max = Vmax
xgate.divs = Vdivs
xgate.tableA = minf / taum
xgate.tableB = 1.0 / taum
ygate = moose.element(CaT.path + '/gateY')
ygate.min = Vmin
ygate.max = Vmax
ygate.divs = Vdivs
ygate.tableA = hinf / tauh
ygate.tableB = 1.0 / tauh
zgate = moose.element(CaT.path + '/gateZ')
zgate.min = Camin
zgate.max = Camax
zgate.divs = Cadivs
ca = np.arange(Camin, Camax + dCa, dCa)
zgate.tableA = ki / (ki + ca)
zgate.tableB = ki / (ki + ca)
#Does not activate calcium-dependent currents
addmsg4 = moose.Mstring(CaT.path + '/addmsg4')
addmsg4.value = '../Ca_conc concOut . concen'
return CaT
def KSK_Chan(name):
KSK = moose.HHChannel('/library/' + name)
KSK.Ek = EK
KSK.Gbar = 300.0 * SOMA_A
KSK.Gk = 0.0
KSK.Xpower = 0.0
KSK.Ypower = 0.0
KSK.Zpower = 1.0
KSK.useConcentration = 1
celsius = 36
cac = 0.56e-3
taumin = 6.3e-3
ca = np.arange(Camin, Camax + dCa, dCa)
car = (ca / cac)**4.6
m_inf = car / (1 + car)
tau_m = taumin + 0 * ca
zgate = moose.element(KSK.path + '/gateZ')
zgate.min = Camin
zgate.max = Camax
zgate.divs = Cadivs
zgate.tableA = m_inf / tau_m
zgate.tableB = 1.0 / tau_m
addmsg3 = moose.Mstring(KSK.path + '/addmsg3')
addmsg3.value = '../Ca_conc concOut . concen'
return KSK
def K_BK_Chan(name):
K_BK = moose.HHChannel2D( '/library/' + name )
K_BK.Ek = EK
K_BK.Gbar = 300.0*SOMA_A
K_BK.Gk = 0.0
K_BK.Xpower = 0.0
K_BK.Ypower = 0.0
K_BK.Zpower = 1.0
K_BK.Zindex = 'VOLT_C1_INDEX'
zgate = moose.element( K_BK.path + '/gateZ' )
zgate.xminA = Vmin
zgate.xmaxA = Vmax
zgate.xdivsA = Vdivs
zgate.yminA = Camin
zgate.ymaxA = Camax
zgate.ydivsA = Cadivs
zgate.xminB = Vmin
zgate.xmaxB = Vmax
zgate.xdivsB = Vdivs
zgate.yminB = Camin
zgate.ymaxB = Camax
zgate.ydivsB = Cadivs
zgate.tableA = tblA*1e3
zgate.tableB = tblB*1e3
addmsg4 = moose.Mstring( K_BK.path + '/addmsg4' )
addmsg4.value = '../Ca_conc concOut . concen'
return K_BK
def Ca_LVAst_Chan(name):
Ca_LVAst = moose.HHChannel( '/library/' + name )
Ca_LVAst.Ek = ECa
Ca_LVAst.Gbar = 300.0*SOMA_A
Ca_LVAst.Gk = 0.0
Ca_LVAst.Xpower = 2.0
Ca_LVAst.Ypower = 1.0
Ca_LVAst.Zpower = 0.0
qt = 2.3**((34-21)/10)
V = v+0.010 #Because Hay2011 shifted this
mInf = 1.0000/(1+ np.exp((V*1e3 - -30.000)/-6))
mTau = (5.0000 + 20.0000/(1+np.exp((V*1e3 - -25.000)/5)))/qt
hInf = 1.0000/(1+ np.exp((V*1e3 - -80.000)/6.4))
hTau = (20.0000 + 50.0000/(1+np.exp((V*1e3 - -40.000)/7)))/qt
xgate = moose.element( Ca_LVAst.path + '/gateX' )
xgate.min = Vmin
xgate.max = Vmax
xgate.divs = Vdivs
xgate.tableA = mInf/mTau*1e3
xgate.tableB = 1/mTau*1e3
ygate = moose.element( Ca_LVAst.path + '/gateY' )
ygate.min = Vmin
ygate.max = Vmax
ygate.divs = Vdivs
ygate.tableA = hInf/hTau*1e3
ygate.tableB = 1/hTau*1e3
addmsg2 = moose.Mstring( Ca_LVAst.path + '/addmsg2' )
addmsg2.value = '. IkOut ../Ca_conc current'
return Ca_LVAst
def simpChan(name):
simp = moose.HHChannel('/library/' + name)
simp.Ek = Ek_K
simp.Gbar = 150 * SOMA_A
simp.Gk = 0
simp.Xpower = 0
simp.Ypower = 0
simp.Zpower = 1
simp.instant = 4
simp.useConcentration = 1
zgate = moose.element(simp.path + '/gateZ')
zgate.min = Camin
zgate.max = Camax
zgate.divs = Cadivs
zA = np.zeros((zgate.divs + 1), dtype=float)
zB = np.zeros((zgate.divs + 1), dtype=float)
dx = (zgate.max - zgate.min) / zgate.divs
x = zgate.min
for i in range(zgate.divs + 1):
zA[i] = min(1.0, x /
zgate.max) #in the paper, its zA[i] = min( 1.0, x/250 )
# zA[i] = min( 1.0, x/250 )
zB[i] = 1.0
x += dx
zgate.tableA = zA
zgate.tableB = zB
addmsg1 = moose.Mstring(simp.path + '/addmsg1')
addmsg1.value = '../Ca_conc concOut . concen'
return simp
def Ca_HVA_Chan(name):
Ca_HVA = moose.HHChannel('/library/' + name)
Ca_HVA.Ek = ECa
Ca_HVA.Gbar = 300.0 * SOMA_A
Ca_HVA.Gk = 0.0
Ca_HVA.Xpower = 2.0
Ca_HVA.Ypower = 1.0
Ca_HVA.Zpower = 0.0
mAlpha = (0.055 * (-27 - v * 1e3)) / (np.exp((-27 - v * 1e3) / 3.8) - 1)
mBeta = (0.94 * np.exp((-75 - v * 1e3) / 17))
hAlpha = (0.000457 * np.exp((-13 - v * 1e3) / 50))
hBeta = (0.0065 / (np.exp((-v * 1e3 - 15) / 28) + 1))
xgate = moose.element(Ca_HVA.path + '/gateX')
xgate.min = Vmin
xgate.max = Vmax
xgate.divs = Vdivs
xgate.tableA = mAlpha * 1e3
xgate.tableB = (mAlpha + mBeta) * 1e3
ygate = moose.element(Ca_HVA.path + '/gateY')
ygate.min = Vmin
ygate.max = Vmax
ygate.divs = Vdivs
ygate.tableA = hAlpha * 1e3
ygate.tableB = (hAlpha + hBeta) * 1e3
addmsg2 = moose.Mstring(Ca_HVA.path + '/addmsg2')
addmsg2.value = '. IkOut ../Ca_conc current'
return Ca_HVA
def KSK_Chan(name):
KSK = moose.HHChannel('/library/' + name)
KSK.Ek = EK
KSK.Gbar = 300.0 * SOMA_A
KSK.Gk = 0.0
KSK.Xpower = 0.0
KSK.Ypower = 0.0
KSK.Zpower = 3.0
KSK.useConcentration = 1
celsius = 36
gbar = 0.01
beta = 0.03e3
cac = 0.025 #Seems too high to me
# cac = 0.00075 #Its mentioned somewhere in the modelDB. So, try this too
taumin = 5e-3
tadj = 3**((celsius - 22.0) / 10)
ca = np.arange(Camin, Camax + dCa, dCa)
car = (ca / cac)**2
m_inf = car / (1 + car)
tau_m = 1 / beta / (1 + car) / tadj
tau_m[tau_m < taumin] = taumin
zgate = moose.element(KSK.path + '/gateZ')
zgate.min = Camin
zgate.max = Camax
zgate.divs = Cadivs
zgate.tableA = m_inf / tau_m
zgate.tableB = 1.0 / tau_m
addmsg3 = moose.Mstring(KSK.path + '/addmsg3')
addmsg3.value = '../Ca_conc concOut . concen'
return KSK
def K_BK_Chan(name):
K_BK = moose.HHChannel2D('/library/' + name)
K_BK.Ek = EK
K_BK.Gbar = 300.0 * SOMA_A
K_BK.Gk = 0.0
K_BK.Xpower = 0.0
K_BK.Ypower = 0.0
K_BK.Zpower = 1.0
K_BK.Zindex = 'VOLT_C1_INDEX'
# cai = 5.e-5
# d1 = .84
# d2 = 1.
# k1 = .48e-3
# k2 = .13e-6
# abar = .28
# bbar = .48
# st=1
# tfactor = 1
# F_KC = F/1000.0
#
# def exp1(k,d,v):
# return k*np.exp(-2*d*F_KC*v*1e3/R/(273.15 + celsius))
# def alp(v,c):
# return c*abar/(c + exp1(k1,d1,v))
# def bet(v,c):
# return bbar/(1 + c/exp1(k2,d2,v))
zgate = moose.element(K_BK.path + '/gateZ')
zgate.xminA = Vmin
zgate.xmaxA = Vmax
zgate.xdivsA = Vdivs
zgate.yminA = Camin
zgate.ymaxA = Camax
zgate.ydivsA = Cadivs
zgate.xminB = Vmin
zgate.xmaxB = Vmax
zgate.xdivsB = Vdivs
zgate.yminB = Camin
zgate.ymaxB = Camax
zgate.ydivsB = Cadivs
# x = Vmin
# tblA = np.zeros([len(v),len(ca)])
# tblB = np.zeros([len(v),len(ca)])
# for i in np.arange(len(v)):
# tblA[i] = np.array([alp(x,y) for y in ca])
# tblB[i] = np.add(tblA[i],[bet(x, y) for y in ca])/tfactor
# x = x + dV
# print(i, end='\r')
#
# zgate.tableA = tblA*1e3
# zgate.tableB = tblB*1e3
zgate.tableA = tblA
zgate.tableB = tblB
addmsg4 = moose.Mstring(K_BK.path + '/addmsg4')
addmsg4.value = '../Ca_conc concOut . concen'
return K_BK
def KahpChan( name ):
Kahp = moose.HHChannel( '/library/' + name )
Kahp.Ek = -0.015 + EREST
Kahp.Gbar = 8*SOMA_A
Kahp.Gk = 0
Kahp.Xpower = 0
Kahp.Ypower = 0
Kahp.Zpower = 1
Kahp.useConcentration = 1 #changed from Kahp.useConcentration = 0
zgate = moose.element( Kahp.path + '/gateZ' )
zgate.min = Camin
zgate.max = Camax
zgate.divs = Cadivs
zA = np.zeros( (zgate.divs + 1), dtype=float)
zB = np.zeros( (zgate.divs + 1), dtype=float)
dx = (zgate.max - zgate.min)/zgate.divs
x = zgate.min
for i in range( zgate.divs + 1 ):
zA[i] = min( 250.00 * x, 10 ) #in paper, its zA[i] = min( 0.02 * x, 10 )
zB[i] = 1.0 + zA[i] #changed from zB[i] = 1.0
x = x + dx
zgate.tableA = zA
zgate.tableB = zB
addmsg1 = moose.Mstring( Kahp.path + '/addmsg1' )
addmsg1.value = '../Ca_conc concOut . concen'
return Kahp
def make_K_AHP():
if moose.exists('K_AHP'):
return
K_AHP = moose.HHChannel('K_AHP')
K_AHP.Ek = EK # V
K_AHP.Gbar = 8 * SOMA_A # S
K_AHP.Gk = 0 # S
K_AHP.Xpower = 0
K_AHP.Ypower = 0
K_AHP.Zpower = 1
zgate = moose.element('K_AHP/gateZ')
xmax = 500.0
zgate.min = 0
zgate.max = xmax
zgate.divs = 3000
zA = numpy.zeros((zgate.divs + 1), dtype=float)
zB = numpy.zeros((zgate.divs + 1), dtype=float)
dx = (zgate.max - zgate.min) / zgate.divs
x = zgate.min
for i in range(zgate.divs + 1):
if (x < (xmax / 2.0)):
zA[i] = 0.02 * x
else:
zA[i] = 10.0
zB[i] = zA[i] + 1.0
x = x + dx
zgate.tableA = zA
zgate.tableB = zB
addmsg1 = moose.Mstring('/library/K_AHP/addmsg1')
addmsg1.value = '../Ca_conc concOut . concen'
def Ca_R_Chan(name):
Ca_R = moose.HHChannel( '/library/' + name )
Ca_R.Ek = ECa
Ca_R.Gbar = 300.0*SOMA_A
Ca_R.Gk = 0.0
Ca_R.Xpower = 3.0
Ca_R.Ypower = 1.0
Ca_R.Zpower = 0.0
minf = 1 / (1 + np.exp((v*1e3+60)/(-3)))
taum = 100 + 0*v*1e3
hinf = 1/ (1 + np.exp((v*1e3+62)/(1)))
tauh = 5 + 0*v*1e3
xgate = moose.element( Ca_R.path + '/gateX' )
xgate.min = Vmin
xgate.max = Vmax
xgate.divs = Vdivs
xgate.tableA = minf/taum*1e3
xgate.tableB = 1.0/taum*1e3
ygate = moose.element( Ca_R.path + '/gateY' )
ygate.min = Vmin
ygate.max = Vmax
ygate.divs = Vdivs
ygate.tableA = hinf/tauh*1e3
ygate.tableB = 1.0/tauh*1e3
addmsg1 = moose.Mstring( Ca_R.path + '/addmsg1' )
addmsg1.value = '. IkOut ../Ca_conc current'
return Ca_R
def make_K_AHP( name ):
if moose.exists( '/library/' + name ):
return
K_AHP = moose.HHChannel( '/library/' + name )
K_AHP.Ek = EK # V
K_AHP.Gbar = 8 * SOMA_A # S
K_AHP.Gk = 0 # S
K_AHP.Xpower = 0
K_AHP.Ypower = 0
K_AHP.Zpower = 1
K_AHP.useConcentration = 1
zgate = moose.element( K_AHP.path + '/gateZ' )
xmax = 0.02 # 20 micromolar.
zgate.min = 0
zgate.max = xmax
zgate.divs = 3000
zA = np.zeros( (zgate.divs + 1), dtype=float)
zB = np.zeros( (zgate.divs + 1), dtype=float)
dx = (zgate.max - zgate.min)/zgate.divs
x = zgate.min
for i in range( zgate.divs + 1 ):
zA[i] = min( 250.00 * CA_SCALE * x, 10 )
zB[i] = 1.0 + zA[i]
x = x + dx
zgate.tableA = zA
zgate.tableB = zB
addmsg1 = moose.Mstring( K_AHP.path + '/addmsg1' )
addmsg1.value = '../Ca_conc concOut . concen'
def K_SK_Chan(name):
K_SK = moose.HHChannel('/library/' + name)
K_SK.Ek = EK
K_SK.Gbar = 300.0 * SOMA_A
K_SK.Gk = 0.0
K_SK.Xpower = 0
K_SK.Ypower = 0
K_SK.Zpower = 3
K_SK.useConcentration = 1
cai = 2.4e-5
gbar = 0.01
beta = 0.03
cac = 0.00035
taumin = 0.5
q10 = 3
tadj = q10**((celsius - 22.0) / 10)
car = (ca / cac)**4
m_inf = car / (1 + car)
tau_m = 1 / beta / (1 + car) / tadj
tau_m[tau_m < taumin] = taumin
zgate = moose.element(K_SK.path + '/gateZ')
zgate.min = Camin
zgate.max = Camax
zgate.divs = Cadivs
zgate.tableA = m_inf / tau_m * 1e3
zgate.tableB = 1.0 / tau_m * 1e3
addmsg3 = moose.Mstring(K_SK.path + '/addmsg3')
addmsg3.value = '../Ca_conc concOut . concen'
return K_SK
def K_SK_Chan(name):
K_SK = moose.HHChannel('/library/' + name)
K_SK.Ek = EK
K_SK.Gbar = 300.0 * SOMA_A
K_SK.Gk = 0.0
K_SK.Xpower = 0.0
K_SK.Ypower = 0.0
K_SK.Zpower = 3.0
K_SK.useConcentration = 1
n = 4
cai = 50.e-6
a0 = 1.3e13
b0 = .5e-2
tfactor = 1
cahalf = 140.04e-6
k = 0.10857
alp = a0 * ca**n
a = alp
tau = tfactor * 1 / (a + b0)
inf = 1 / (1 + np.exp((np.log(cahalf / ca)) / k))
zgate = moose.element(K_SK.path + '/gateZ')
zgate.min = Camin
zgate.max = Camax
zgate.divs = Cadivs
zgate.tableA = inf / tau * 1e3
zgate.tableB = 1.0 / tau * 1e3
addmsg3 = moose.Mstring(K_SK.path + '/addmsg3')
addmsg3.value = '../Ca_conc concOut . concen'
return K_SK
def CaT_Chan(name):
CaT = moose.HHChannel('/library/' + name)
CaT.Ek = ECa
CaT.Gbar = 300.0 * SOMA_A
CaT.Gk = 0.0
CaT.Xpower = 2.0
CaT.Ypower = 1.0
CaT.Zpower = 0.0
celsius = 25
gcatbar = .003
cao = 2
q10 = 5
mmin = 0.2
hmin = 10
a0h = 0.015
zetah = 3.5
vhalfh = -70.018017
gmh = 0.6
a0m = 0.04
zetam = 2
vhalfm = -17.868123
gmm = 0.61
vhm = -60
vhh = -85
mtfactor = 1.552435
htfactor = 0.963171
alph = np.exp(0.0378 * zetah * (v * 1e3 - vhalfh))
beth = np.exp(0.0378 * zetah * gmh * (v * 1e3 - vhalfh))
alpmt = np.exp(0.0378 * zetam * (v * 1e3 - vhalfm))
betmt = np.exp(0.0378 * zetam * gmm * (v * 1e3 - vhalfm))
qt = q10**((celsius - 25) / 10)
minf = (1 / (1 + np.exp(-(v * 1e3 - vhm) / 10)))
mtau = mtfactor * betmt / (qt * a0m * (1 + alpmt)) * 1e-3
mtau[mtau < mmin * 1e-3] = mmin * 1e-3
hinf = (1 / (1 + np.exp((v * 1e3 - vhh) / 10)))
htau = htfactor * beth / (a0h * (1 + alph)) * 1e-3
htau[htau < hmin * 1e-3] = hmin * 1e-3
xgate = moose.element(CaT.path + '/gateX')
xgate.min = Vmin
xgate.max = Vmax
xgate.divs = Vdivs
xgate.tableA = minf / mtau
xgate.tableB = 1.0 / mtau
ygate = moose.element(CaT.path + '/gateY')
ygate.min = Vmin
ygate.max = Vmax
ygate.divs = Vdivs
ygate.tableA = hinf / htau
ygate.tableB = 1.0 / htau
addmsg1 = moose.Mstring(CaT.path + '/addmsg1')
addmsg1.value = '. IkOut ../Ca_conc current'
return CaT
def KBK_Chan(name):
KBK = moose.HHChannel2D('/library/' + name)
KBK.Ek = EK
KBK.Gbar = 300.0 * SOMA_A
KBK.Gk = 0.0
KBK.Xpower = 0.0
KBK.Ypower = 0.0
KBK.Zpower = 1.0
KBK.Zindex = 'VOLT_C1_INDEX'
cai = 5.e-5
d1 = .84
d2 = 1.
k1 = 0.000588
k2 = 8.76481e-08
abar = .28
bbar = .48
st = 1
tfactor = 1.279493
F_KC = F / 1000.0
def exp1(k, d, v):
return k * np.exp(-2 * d * F_KC * v * 1e3 / R / (273.15 + celsius))
def alp(v, c):
return c * abar / (c + exp1(k1, d1, v))
def bet(v, c):
return bbar / (1 + c / exp1(k2, d2, v))
zgate = moose.element(KBK.path + '/gateZ')
zgate.xminA = Vmin
zgate.xmaxA = Vmax
zgate.xdivsA = Vdivs
zgate.yminA = Camin
zgate.ymaxA = Camax
zgate.ydivsA = Cadivs
zgate.xminB = Vmin
zgate.xmaxB = Vmax
zgate.xdivsB = Vdivs
zgate.yminB = Camin
zgate.ymaxB = Camax
zgate.ydivsB = Cadivs
x = Vmin
tblA = np.zeros([len(v), len(ca)])
tblB = np.zeros([len(v), len(ca)])
for i in np.arange(len(v)):
tblA[i] = np.array([alp(x, y) for y in ca])
tblB[i] = np.add(tblA[i], [bet(x, y) for y in ca]) / tfactor
x = x + dV
print(i, end='\r')
zgate.tableA = tblA * 1e3
zgate.tableB = tblB * 1e3
addmsg4 = moose.Mstring(KBK.path + '/addmsg4')
addmsg4.value = '../Ca_conc concOut . concen'
return KBK
def readSynapseML(self, synapseElement, units="SI units"):
# see pg 219 (sec 13.2) of Book of Genesis
if 'Physiological Units' in units:
Vfactor = 1e-3 # V from mV
Tfactor = 1e-3 # s from ms
Gfactor = 1e-3 # S from mS
elif 'SI Units' in units:
Vfactor = 1.0
Tfactor = 1.0
Gfactor = 1.0
else:
debug.printDebug("ERROR", "Wrong units {0}".format(units))
raise UserWarning, "Wrong value or parameter {0}".format(units)
# creates /library in MOOSE tree; elif present, wraps
# NOTE: This path is created by NeuroML now in __init__. Disabling,
# Dilawar Singh
#moose.Neutral(self.libraryPath+'')
if utils.neuroml_debug:
synName = synapseElement.attrib['name']
msg = "Loading synapse : %s into library ." % synName
debug.printDebug("INFO", msg)
self.mooseSynp = moose.SynChan(
os.path.join(self.libraryPath, synapseElement.attrib['name']))
doub_exp_syn = synapseElement.find('./{' + self.cml + '}doub_exp_syn')
self.mooseSynp.Ek = float(doub_exp_syn.attrib['reversal_potential']) \
* Vfactor
self.mooseSynp.Gbar = float(doub_exp_syn.attrib['max_conductance'])\
* Gfactor
# seconds
self.mooseSynp.tau1 = float(doub_exp_syn.attrib['rise_time']) * Tfactor
# second\s
self.mooseSynp.tau2 = float(
doub_exp_syn.attrib['decay_time']) * Tfactor
# The delay and weight can be set only after connecting a spike event
# generator. delay and weight are arrays: multiple event messages can
# be connected to a single synapse
self.mooseSynp_graded = moose.Mstring(self.mooseSynp.path + '/graded')
self.mooseSynp_graded.value = 'False'
self.mooseSynp_mgblock = moose.Mstring(self.mooseSynp.path +
'/mgblock')
self.mooseSynp_mgblock.value = 'False'
def make_vclamp( name = 'Vclamp', parent = '/library' ):
if moose.exists( '/library/' + name ):
return
vclamp = moose.VClamp( parent + '/' + name )
vclamp.mode = 0 # Default. could try 1, 2 as well
vclamp.tau = 0.2e-3 # lowpass filter for command voltage input
vclamp.ti = 20e-6 # Integral time
vclamp.td = 5e-6 # Differential time. Should it be >= dt?
vclamp.gain = 0.00005 # Gain of vclamp ckt.
# Connect voltage clamp circuitry
addmsg1 = moose.Mstring( vclamp.path + '/addmsg1' )
addmsg1.value = '. currentOut .. injectMsg'
addmsg2 = moose.Mstring( vclamp.path + '/addmsg2' )
addmsg2.value = '.. VmOut . sensedIn'
return vclamp
