def makeChemProto(name='hydra'):
chem=moose.Neutral('/library/'+name)
compt=moose.CubeMesh('/library/'+name + '/' + name)
A=moose.Pool(compt.path+'/A')
B=moose.Pool(compt.path+'/B')
#A.diffConst=params['diffA']
#B.diffConst=params['diffB']
Adot = moose.Function( A.path + '/Adot' )
Bdot = moose.Function( B.path + '/Bdot' )
Adot.expr="-x0+(x0^2/(1+0.01*x0^2))*x1"
Bdot.expr="x0-(x0^2/(1+0.01*x0^2))*x1"
print moose.showmsg(Adot)
Adot.x.num = 2 #2
Bdot.x.num = 2 #2
moose.connect( A, 'nOut', Adot.x[0], 'input' )
moose.connect( B, 'nOut', Adot.x[1], 'input' )
moose.connect( Adot, 'valueOut', A, 'increment' )
moose.connect( A, 'nOut', Bdot.x[0], 'input' )
moose.connect( B, 'nOut', Bdot.x[1], 'input' )
moose.connect( Bdot, 'valueOut', B, 'increment' )
def makeChemProto(name='hydra'):
chemCompt = moose.Neutral('/library/' + name)
compt = moose.CubeMesh('/library/' + name + '/' + name)
A = moose.Pool(compt.path + '/A')
B = moose.Pool(compt.path + '/B')
Adot = moose.Function(A.path + '/Adot')
Bdot = moose.Function(B.path + '/Bdot')
#Adot.expr="1*(-x0+x1*(0.05*+(x0^2/(1^2+x0^2))))"
#Bdot.expr="-1*(-x0+x1*(0.05*+(x0^2/(1^2+x0^2))))"
Adot.expr = "0*x0+0*x1"
Bdot.expr = "0*x0+0*x1"
print "$$$$> ", Adot, Bdot
print Adot.expr, Bdot.expr
print moose.showmsg(Adot)
Adot.x.num = 2
Bdot.x.num = 2
A.nInit = 1
B.nInit = 1
moose.connect(A, 'nOut', Adot.x[0], 'input')
moose.connect(B, 'nOut', Adot.x[1], 'input')
moose.connect(Adot, 'valueOut', A, 'increment')
moose.connect(A, 'nOut', Bdot.x[0], 'input')
moose.connect(B, 'nOut', Bdot.x[1], 'input')
moose.connect(Bdot, 'valueOut', B, 'increment')
return compt
def makeChemProto(name='hydra'):
chem = moose.Neutral('/library/' + name)
compt = moose.CubeMesh('/library/' + name + '/' + name)
A = moose.Pool(compt.path + '/A')
B = moose.Pool(compt.path + '/B')
#A.diffConst=params['diffA']
#B.diffConst=params['diffB']
Adot = moose.Function(A.path + '/Adot')
Bdot = moose.Function(B.path + '/Bdot')
Adot.expr = "11.8*x1-x0+0"
Bdot.expr = "x0-(0.1*x1^3-6.3*x1^2+100*x1)"
#Adot.expr="x0+0.0001*x1^3"
#Bdot.expr="x0-0.001*x1^3"
#Adot.expr="0.0000118*x1-0.000001x0"
#Bdot.expr="x0-0.0000001*x1^3-0.0000063*x1^2+0.001*x1"
print "$$$$> ", Adot, Bdot
print Adot.expr, Bdot.expr
print moose.showmsg(Adot)
Adot.x.num = 2 #2
Bdot.x.num = 2 #2
A.nInit = 0.01
B.nInit = 10
moose.connect(A, 'nOut', Adot.x[0], 'input')
moose.connect(B, 'nOut', Adot.x[1], 'input')
moose.connect(Adot, 'valueOut', A, 'increment')
moose.connect(A, 'nOut', Bdot.x[0], 'input')
moose.connect(B, 'nOut', Bdot.x[1], 'input')
moose.connect(Bdot, 'valueOut', B, 'increment')
return compt
def makeChemProto(name='hydra'):
chem = moose.Neutral('/library/' + name)
compt = moose.CubeMesh('/library/' + name + '/' + name)
A = moose.Pool(compt.path + '/A')
B = moose.Pool(compt.path + '/B')
Adot = moose.Function(A.path + '/Adot')
Bdot = moose.Function(B.path + '/Bdot')
Adot.expr = "k*(b*(0.05*+(a^n/(K^n+a^n)))-a)"
Bdot.expr = "-k*(b*(0.05*+(a^n/(K^n+a^n)))-a)"
print "$$$$> ", Adot, Bdot
print Adot.expr, Bdot.expr
print moose.showmsg(Adot)
Adot.x.num = 3 #2
Bdot.x.num = 3 #2
A.nInit = 1
B.nInit = 1
moose.connect(A, 'nOut', Adot.x[0], 'input')
moose.connect(B, 'nOut', Adot.x[1], 'input')
moose.connect(Adot, 'valueOut', A, 'increment')
moose.connect(A, 'nOut', Bdot.x[0], 'input')
moose.connect(B, 'nOut', Bdot.x[1], 'input')
moose.connect(Bdot, 'valueOut', B, 'increment')
return compt
def makeChemProto(name='hydra'):
chem = moose.Neutral('/library/' + name)
compt = moose.CubeMesh('/library/' + name + '/' + name)
A = moose.Pool(compt.path + '/A')
B = moose.Pool(compt.path + '/B')
C = moose.Pool(compt.path + '/C')
space = moose.Pool(compt.path + '/space')
#A.diffConst=params['diffA']
#B.diffConst=params['diffB']
Adot = moose.Function(A.path + '/Adot')
Bdot = moose.Function(B.path + '/Bdot')
Cdot = moose.Function(C.path + '/Cdot')
#Adot.expr="0.001*((x0^2/x1)+1)-1*x0+0.5*x0"
#Bdot.expr="0*x0+0.001*x0^2-1*x1+1*x1"
Adot.expr = "0.5*exp(-1.5*x2/(50*1e-06))*x0^2*x1-(0.1+0.01)*x0+0.01*x1"
Bdot.expr = "-0.5*exp(-1.5*x2/(50*1e-06))*x0^2*x1+0.1*x0-0.01*x1+0.01"
print moose.showmsg(Adot)
Adot.x.num = 3 #2
Bdot.x.num = 3 #2
#A.nInit=10
#B.nInit=5
A.nInit = 0
B.nInit = 0
moose.connect(A, 'nOut', Adot.x[0], 'input')
moose.connect(B, 'nOut', Adot.x[1], 'input')
moose.connect(space, 'nOut', Adot.x[2], 'input')
moose.connect(Adot, 'valueOut', A, 'increment')
moose.connect(A, 'nOut', Bdot.x[0], 'input')
moose.connect(B, 'nOut', Bdot.x[1], 'input')
moose.connect(space, 'nOut', Bdot.x[2], 'input')
moose.connect(Bdot, 'valueOut', B, 'increment')
return compt
def main():
soma_l = 50E-6
soma_d = 25E-6
soma_RM = 1 #20000
soma_CM = 10E-3 #1E-6
soma_RA = 4.0
simtime = 300E-3 # seconds
simdt = 1E-3 #50E-6 # seconds
soma = create_compartment('soma', soma_l, soma_d, soma_RM, soma_CM,
soma_RA)
soma.Em = -65E-3
soma.initVm = -65E-3
inj_duration = 100E-3
inj_amplitude = 1E-9 #0.188E-9
pulse_1 = create_pulse_generator(soma, inj_duration, inj_amplitude)
vmtab = create_output_table()
moose.connect(vmtab, 'requestOut', soma, 'getVm')
moose.showmsg(soma)
#moose.setClock(4, simdt)
moose.reinit()
moose.start(simtime)
plot_vm_table(vmtab, simtime, simdt)
plt.axvline(x=50E-3 + soma_RM * soma_CM, color='red')
plt.show()
def makeChemProto(name='hydra'):
chem = moose.Neutral('/library/' + name)
compt = moose.CubeMesh('/library/' + name + '/' + name)
A = moose.Pool(compt.path + '/A')
B = moose.Pool(compt.path + '/B')
#A.diffConst=params['diffA']
#B.diffConst=params['diffB']
Adot = moose.Function(A.path + '/Adot')
Bdot = moose.Function(B.path + '/Bdot')
#Adot.expr="0.001*((x0^2/x1)+1)-1*x0+0.5*x0"
#Bdot.expr="0*x0+0.001*x0^2-1*x1+1*x1"
Adot.expr = "0.1*((x0^2/x1)+1)-1.5*x0+0.5*x0"
Bdot.expr = "0*x0+0.1*x0^2-1.5*x1+1*x1"
print "$$$$> ", Adot, Bdot
print Adot.expr, Bdot.expr
print moose.showmsg(Adot)
Adot.x.num = 2 #2
Bdot.x.num = 2 #2
#A.nInit=10
#B.nInit=5
A.nInit = 1
B.nInit = 1
moose.connect(A, 'nOut', Adot.x[0], 'input')
moose.connect(B, 'nOut', Adot.x[1], 'input')
moose.connect(Adot, 'valueOut', A, 'increment')
moose.connect(A, 'nOut', Bdot.x[0], 'input')
moose.connect(B, 'nOut', Bdot.x[1], 'input')
moose.connect(Bdot, 'valueOut', B, 'increment')
return compt
def run(nogui):
reader = NML2Reader(verbose=True)
filename = 'test_files/passiveCell.nml'
print('Loading: %s'%filename)
reader.read(filename)
msoma = reader.getComp(reader.doc.networks[0].populations[0].id,0,0)
print(msoma)
data = moose.Neutral('/data')
pg = reader.getInput('pulseGen1')
inj = moose.Table('%s/pulse' % (data.path))
moose.connect(inj, 'requestOut', pg, 'getOutputValue')
vm = moose.Table('%s/Vm' % (data.path))
moose.connect(vm, 'requestOut', msoma, 'getVm')
simdt = 1e-6
plotdt = 1e-4
simtime = 150e-3
if (1):
#moose.showmsg( '/clock' )
for i in range(8):
moose.setClock( i, simdt )
moose.setClock( 8, plotdt )
moose.reinit()
else:
utils.resetSim([model.path, data.path], simdt, plotdt, simmethod='ee')
moose.showmsg( '/clock' )
moose.start(simtime)
print("Finished simulation!")
t = np.linspace(0, simtime, len(vm.vector))
if not nogui:
import matplotlib.pyplot as plt
plt.subplot(211)
plt.plot(t, vm.vector * 1e3, label='Vm (mV)')
plt.legend()
plt.title('Vm')
plt.subplot(212)
plt.title('Input')
plt.plot(t, inj.vector * 1e9, label='injected (nA)')
#plt.plot(t, gK.vector * 1e6, label='K')
#plt.plot(t, gNa.vector * 1e6, label='Na')
plt.legend()
plt.show()
plt.close()
def desensitization(synchan, SynParams):
'''
Key equations to be implemented
dep.expression = "x = x*"+str(dep_constant)+"y*"+str(SynParams.dep_per_spike)
weight.expression = "weight*1/(1+x)/simdt"
facsynchan uses: (1+fac)/(1+dep)/simdt
x above is dep, and we didn't have fac, hence 1/(1+x)
weight is the current synaptic weight
'''
sh = moose.element(synchan).children[0]
deppath = synchan.path + '/dep'
weightpath = synchan.path + '/weight'
dep = moose.Func(deppath)
weight = moose.Func(weightpath)
help_dep = moose.Func(deppath + "/help")
activation = moose.Func(deppath + "/activation")
activation_help = moose.Func(deppath + "/activation/help")
y = moose.Func(deppath + "/y")
condition = moose.Func(deppath + "/condition")
help_dep.tick = synchan.tick
dep.tick = synchan.tick
weight.tick = synchan.tick
activation.tick = synchan.tick
activation_help.tick = synchan.tick
y.tick = synchan.tick
condition.tick = synchan.tick
#x*exp(dt/tau)+y*dep_per_spike, where x is output of self!
dep_const = np.exp(-synchan.dt / SynParams.dep_tau)
dep.expr = "x*" + str(dep_const) + "+y*" + str(SynParams.dep_per_spike)
help_dep.expr = "x"
weight.expr = "z*(1./(1+x))/" + str(synchan.dt)
activation.expr = "x+y"
activation_help.expr = "x"
y.expr = "x"
condition.expr = "x&&(x==y)"
moose.connect(dep, "valueOut", weight, "xIn")
moose.connect(condition, 'valueOut', dep, 'yIn')
moose.connect(condition, 'valueOut', weight, 'zIn')
moose.connect(condition, 'valueOut', activation, 'zIn')
moose.connect(sh, 'activationOut', activation, 'yIn')
moose.connect(sh, 'activationOut', y, 'xIn')
moose.connect(activation, "valueOut", condition, "xIn")
moose.connect(y, "valueOut", condition, "yIn")
moose.connect(condition, "valueOut", y, "zIn")
moose.connect(activation, "valueOut", activation_help, "xIn")
moose.connect(activation_help, "valueOut", activation, "xIn")
moose.connect(dep, 'valueOut', help_dep, 'xIn')
moose.connect(help_dep, 'valueOut', dep, 'xIn')
moose.connect(weight, "valueOut", synchan, 'activation')
moose.showmsg(synchan)
return condition, activation
def run(nogui):
reader = NML2Reader(verbose=True)
filename = 'test_files/passiveCell.nml'
print('Loading: %s' % filename)
reader.read(filename)
msoma = reader.getComp(reader.doc.networks[0].populations[0].id, 0, 0)
print(msoma)
data = moose.Neutral('/data')
pg = reader.getInput('pulseGen1')
inj = moose.Table('%s/pulse' % (data.path))
moose.connect(inj, 'requestOut', pg, 'getOutputValue')
vm = moose.Table('%s/Vm' % (data.path))
moose.connect(vm, 'requestOut', msoma, 'getVm')
simdt = 1e-6
plotdt = 1e-4
simtime = 150e-3
if (1):
#moose.showmsg( '/clock' )
for i in range(8):
moose.setClock(i, simdt)
moose.setClock(8, plotdt)
moose.reinit()
else:
utils.resetSim([model.path, data.path], simdt, plotdt, simmethod='ee')
moose.showmsg('/clock')
moose.start(simtime)
print("Finished simulation!")
t = np.linspace(0, simtime, len(vm.vector))
if not nogui:
import matplotlib.pyplot as plt
plt.subplot(211)
plt.plot(t, vm.vector * 1e3, label='Vm (mV)')
plt.legend()
plt.title('Vm')
plt.subplot(212)
plt.title('Input')
plt.plot(t, inj.vector * 1e9, label='injected (nA)')
#plt.plot(t, gK.vector * 1e6, label='K')
#plt.plot(t, gNa.vector * 1e6, label='Na')
plt.legend()
plt.show()
plt.close()
def test_hhcomp():
"""Create and simulate a single spherical compartment with
Hodgkin-Huxley Na and K channel.
Plots Vm, injected current, channel conductances.
"""
model = moose.Neutral('/model')
data = moose.Neutral('/data')
comp, na, k = create_hhcomp(parent=model.path)
print comp.Rm, comp.Cm, na.Ek, na.Gbar, k.Ek, k.Gbar
pg = moose.PulseGen('%s/pg' % (model.path))
pg.firstDelay = 20e-3
pg.firstWidth = 40e-3
pg.firstLevel = 1e-9
pg.secondDelay = 1e9
moose.connect(pg, 'output', comp, 'injectMsg')
inj = moose.Table('%s/pulse' % (data.path))
moose.connect(inj, 'requestOut', pg, 'getOutputValue')
vm = moose.Table('%s/Vm' % (data.path))
moose.connect(vm, 'requestOut', comp, 'getVm')
gK = moose.Table('%s/gK' % (data.path))
moose.connect(gK, 'requestOut', k, 'getGk')
gNa = moose.Table('%s/gNa' % (data.path))
moose.connect(gNa, 'requestOut', na, 'getGk')
simdt = 1e-6
plotdt = 1e-4
simtime = 100e-3
if (1):
moose.showmsg( '/clock' )
for i in range(8):
moose.setClock( i, simdt )
moose.setClock( 8, plotdt )
moose.reinit()
else:
utils.resetSim([model.path, data.path], simdt, plotdt, simmethod='ee')
moose.showmsg( '/clock' )
moose.start(simtime)
t = np.linspace(0, simtime, len(vm.vector))
plt.subplot(211)
plt.plot(t, vm.vector * 1e3, label='Vm (mV)')
plt.plot(t, inj.vector * 1e9, label='injected (nA)')
plt.legend()
plt.title('Vm')
plt.subplot(212)
plt.title('Conductance (uS)')
plt.plot(t, gK.vector * 1e6, label='K')
plt.plot(t, gNa.vector * 1e6, label='Na')
plt.legend()
plt.show()
plt.close()
def desensitization(synchan, SynParams):
sh = moose.element(synchan).children[0]
deppath = synchan.path + '/dep'
weightpath = synchan.path + '/weight'
dep = moose.Func(deppath)
weight = moose.Func(weightpath)
help_dep = moose.Func(deppath + "/help")
activation = moose.Func(deppath + "/activation")
activation_help = moose.Func(deppath + "/activation/help")
y = moose.Func(deppath + "/y")
condition = moose.Func(deppath + "/condition")
help_dep.tick = synchan.tick
dep.tick = synchan.tick
weight.tick = synchan.tick
activation.tick = synchan.tick
activation_help.tick = synchan.tick
y.tick = synchan.tick
condition.tick = synchan.tick
dep_const = np.exp(-synchan.dt / SynParams.dep_tau)
dep.expr = "x*" + str(dep_const) + "+y*" + str(SynParams.dep_per_spike)
help_dep.expr = "x"
weight.expr = "z*(1./(1+x))/" + str(synchan.dt)
activation.expr = "x+y"
activation_help.expr = "x"
y.expr = "x"
condition.expr = "x&&(x==y)"
moose.connect(dep, "valueOut", weight, "xIn")
moose.connect(condition, 'valueOut', dep, 'yIn')
moose.connect(condition, 'valueOut', weight, 'zIn')
moose.connect(condition, 'valueOut', activation, 'zIn')
moose.connect(sh, 'activationOut', activation, 'yIn')
moose.connect(sh, 'activationOut', y, 'xIn')
moose.connect(activation, "valueOut", condition, "xIn")
moose.connect(y, "valueOut", condition, "yIn")
moose.connect(condition, "valueOut", y, "zIn")
moose.connect(activation, "valueOut", activation_help, "xIn")
moose.connect(activation_help, "valueOut", activation, "xIn")
moose.connect(dep, 'valueOut', help_dep, 'xIn')
moose.connect(help_dep, 'valueOut', dep, 'xIn')
moose.connect(weight, "valueOut", synchan, 'activation')
moose.showmsg(synchan)
return condition, activation
def makeChemProto(name='hydra'):
maxs = 0.05
chem = moose.Neutral('/library/' + name)
compt = moose.CubeMesh('/library/' + name + '/' + name)
A = moose.Pool(compt.path + '/A')
B = moose.Pool(compt.path + '/B')
S = moose.Pool(compt.path + '/S')
space = moose.Pool(compt.path + '/space')
#C=moose.Pool(compt.path+'/C')
#A.diffConst=params['diffA']
#B.diffConst=params['diffB']
Adot = moose.Function(A.path + '/Adot')
Bdot = moose.Function(B.path + '/Bdot')
Sdot = moose.Function(S.path + '/Sdot')
spacedot = moose.Function(space.path + '/spacedot')
#Cdot = moose.Function( C.path + '/Cdot' )
#Adot.expr="0.001*((x0^2/x1)+1)-1*x0+0.5*x0"
#Bdot.expr="0*x0+0.001*x0^2-1*x1+1*x1"
#Adot.expr="-x0+x1(0.067+(1*x0^2)/(1+x0^2))"
#Bdot.expr="x0-x1(0.067+(1*x0^2)/(1+x0^2))"
Adot.expr = "-x0+x1*(0.067+(1*x0^2)/(1+x0^2))+(t<20)*(0.05/2)*(1+cos(" + str(
np.pi) + "*x3))*x1*x2+(t>20)*(t<25)*(0.05/4)*(cos(" + str(
np.pi) + "*(t-20)/5))*(1+cos(" + str(np.pi) + "*x3))*x1*x2"
Bdot.expr = "x0-x1*(0.067+(1*x0^2)/(1+x0^2))-(t<20)*(0.05/2)*(1+cos(" + str(
np.pi) + "*x3))*x1*x2-(t>20)*(t<25)*(0.05/4)*(cos(" + str(
np.pi) + "*(t-20)/5))*(1+cos(" + str(np.pi) + "*x3))*x1*x2"
Sdot.expr = "0"
spacedot.expr = "0"
#Cdot.expr="0*x0+0.11*x1-0.11*x2+0.1*x0^2-0.1*(x1+x2)"
print "$$$$> ", Adot, Bdot
print Adot.expr, Bdot.expr
print moose.showmsg(Adot)
Adot.x.num = 4 #2
Bdot.x.num = 4 #2
moose.connect(A, 'nOut', Adot.x[0], 'input')
moose.connect(B, 'nOut', Adot.x[1], 'input')
moose.connect(S, 'nOut', Adot.x[2], 'input')
moose.connect(space, 'nOut', Adot.x[3], 'input')
moose.connect(Adot, 'valueOut', A, 'increment')
moose.connect(A, 'nOut', Bdot.x[0], 'input')
moose.connect(B, 'nOut', Bdot.x[1], 'input')
moose.connect(S, 'nOut', Bdot.x[2], 'input')
moose.connect(space, 'nOut', Bdot.x[3], 'input')
moose.connect(Bdot, 'valueOut', B, 'increment')
return compt
def soma_five_dend():
soma_l = 50E-6
soma_d = 25E-6
soma_RM = 1 #20000
soma_CM = 10E-3 #1E-6
soma_RA = 4.0
simtime = 0.3 # seconds
simdt = 50E-6 #50E-6 # seconds
dend_n = 5
soma = create_compartment('soma', soma_l, soma_d, soma_RM, soma_CM,
soma_RA)
soma_Em = -65E-3
soma_initVm = -65E-3
inj_duration = 100E-3
inj_amplitude = 1E-9 #0.188E-9
pulse_1 = create_pulse_generator(soma, inj_duration, inj_amplitude)
vmtab = create_output_table()
moose.connect(vmtab, 'requestOut', soma, 'getVm')
moose.showmsg(soma)
moose.setClock(4, simdt)
bunch = create_n_dends('dend_', dend_n, 100E-6, 2E-6, soma_RM, soma_CM,
soma_RA)
for item in bunch.values():
item.Em = soma.Em
item.initVm = soma.initVm
bunch = connect_n_serial(bunch)
moose.connect(soma, 'axialOut', list(bunch.values())[0], 'handleAxial')
dend_vm_tab = create_output_table(table_name='dend3Vm')
moose.connect(dend_vm_tab, 'requestOut',
list(bunch.values())[int(np.median(range(len(bunch))))],
'getVm')
moose.reinit()
moose.start(simtime)
plot = plot_vm_table(simtime,
vmtab,
dend_vm_tab,
title="Soma Vs Dend voltage compare.")
plot.legend(['soma', 'dend'])
plt.grid(True)
plt.show()
def test_simple():
"""First test.
>>> test_simple() # doctest: +NORMALIZE_WHITESPACE
Rdesigneur: Elec model has 1 compartments and 0 spines on 0 compartments.
<BLANKLINE>
[/model[0]/elec[0]/soma[0]]
Cm =7.853981633975e-09
Em =-0.0544
Im =1.3194689277024895e-08
Ra =7639437.268410473
Rm =424413.1773342278
Vm =-0.06
className =ZombieCompartment
diameter =0.0005
dt =0.0
fieldIndex =0
idValue =455
index =0
initVm =-0.065
inject =0.0
length =0.0005
name =soma
numData =1
numField =1
path =/model[0]/elec[0]/soma[0]
tick =-2
x =0.0005
x0 =0.0
y =0.0
y0 =0.0
z =0.0
z0 =0.0
<BLANKLINE>
INCOMING:
/model[0]/elec[0]/soma ('parentMsg',) <--- /model[0]/elec ('childOut',)
OUTGOING:
"""
rdes = rd.rdesigneur()
rdes.buildModel()
moose.showfields(rdes.soma)
moose.showmsg(rdes.soma)
def soma_one_dend():
soma_l = 50E-6
soma_d = 25E-6
soma_RM = 1 #20000
soma_CM = 10E-3 #1E-6
soma_RA = 4.0
simtime = 0.3 # seconds
simdt = 50E-6 #50E-6 # seconds
soma = create_compartment('soma', soma_l, soma_d, soma_RM, soma_CM,
soma_RA)
soma_Em = -65E-3
soma_initVm = -65E-3
inj_duration = 100E-3
inj_amplitude = 1E-9 #0.188E-9
pulse_1 = create_pulse_generator(soma, inj_duration, inj_amplitude)
vmtab = create_output_table()
moose.connect(vmtab, 'requestOut', soma, 'getVm')
moose.showmsg(soma)
moose.setClock(4, simdt)
dend1 = create_compartment('dend1', 100E-6, 2E-6, soma_RM, soma_CM,
soma_RA)
dend1.Em = soma.Em
dend1.initVm = soma.initVm
moose.connect(soma, 'axialOut', dend1, 'handleAxial')
dend1_vm_tab = create_output_table(table_name='dend1Vm')
moose.connect(dend1_vm_tab, 'requestOut', dend1, 'getVm')
moose.showmsg(dend1)
moose.reinit()
moose.start(simtime)
plot_vm_table(vmtab, simtime)
plot_vm_table(dend1_vm_tab, simtime)
plt.axvline(x=50E-3 + soma_RM * soma_CM, color='red')
plt.show()
def main():
neuron = moose.Neutral("/neuron")
inputs = moose.Neutral("/inputs")
outputs = moose.Neutral("/outputs")
soma = create_spherical_compartment("/neuron/soma", 25e-6, 20e-6, 2.8, 4.0,
0.03)
pulse = create_pulse('/inputs/somaPulse', 50e-3, 100e-3, 1e-9, soma)
vmtable = create_table('outputs/somaVmTable', soma, "getVm")
print(soma.tick)
print(soma.dt)
moose.reinit()
moose.start(300e-3)
moose.showfields(vmtable)
moose.showmsg(soma)
moose.showmsg(pulse)
moose.showmsg(vmtable)
plot_table(vmtable)
pyplot.show()
model = create_model_sim.setupNeurons(model, network=not net.single)
all_neur_types = model.neurons
# FSIsyn,neuron = cell_proto.neuronclasses(FSI)
# all_neur_types.update(neuron)
population, connections, plas = create_network.create_network(model, net, all_neur_types)
###### Set up stimulation - could be current injection or plasticity protocol
# set num_inject=0 to avoid current injection
if net.num_inject < np.inf:
inject_pop = inject_func.inject_pop(population['pop'], net.num_inject)
else:
inject_pop = population['pop']
# Does setupStim work for network?
# create_model_sim.setupStim(model)
pg = inject_func.setupinj(model, param_sim.injection_delay, param_sim.injection_width, inject_pop)
moose.showmsg(pg)
##############--------------output elements
if net.single:
# fname=model.param_stim.Stimulation.Paradigm.name+'_'+model.param_stim.location.stim_dendrites[0]+'.npz'
# simpath used to set-up simulation dt and hsolver
simpath = ['/' + neurotype for neurotype in all_neur_types]
create_model_sim.setupOutput(model)
else: # population of neurons
spiketab, vmtab, plastab, catab = net_output.SpikeTables(model, population['pop'], net.plot_netvm, plas,
net.plots_per_neur)
# simpath used to set-up simulation dt and hsolver
simpath = [net.netname]
clocks.assign_clocks(simpath, param_sim.simdt, param_sim.plotdt, param_sim.hsolve, model.param_cond.NAME_SOMA)
if model.synYN and (param_sim.plot_synapse or net.single):
# overwrite plastab above, since it is empty
# Looping through synparams dictionary and creates synaptic channels
# Moose uses GHK current equation to solve how calcium affects the NMDA
# channel -- temp, extCa, and condFraction required for solving this
for key, params in synparams.items():
if key == 'nmda':
chan = moose.NMDAChan('/cell2/dend/' + key)
chan.KMg_A = params['mgparams']['A']
chan.KMg_B = params['mgparams']['B']
chan.CMg = params['mgparams']['conc']
chan.temperature = params['temperature']
chan.extCa = params['extCa']
chan.condFraction = params['condFraction']
else:
chan = moose.SynChan('/cell2/dend/' + key)
chan.Gbar = params['Gbar']
chan.tau1 = params['tau1']
chan.tau2 = params['tau2']
chan.Ek = params['Erev']
# Below code is just an example -- in HW we will modify our existing CaPool
# code
capool = moose.CaConc('/cell2/dend/capool')
moose.showfield(capool)
nmdachan = moose.element('/cell2/dend/nmda')
moose.connect(nmdachan, 'ICaOut', capool, 'current')
moose.connect(capool, 'concOut', nmdachan, 'setIntCa')
moose.showmsg(nmdachan)
moose.reinit()
# start simulation at 0 nA injection current.
moose.start(0.3)
moose.showfields(soma) # check Vm
soma.inject = -1E-12
# reset simulation
moose.reint()
# start simulation at -1pA injection current.
moose.start(0.3)
moose.showfields(soma)
# Creation of pulse generator.
pulse = moose.PulseGen('pulse')
moose.showfield('pulse')
pulse.delay[0] = 50E-3 # First delay.
pulse.width[0] = 100E03 # Pulse width.
pulse.level[0] = 1E-9 # Pulse amplitude.
pulse.delat[1] = 1E9
moose.getFieldNames(
'PulseGen',
'srcFinfo') # returns list of message outlets for a moose element class.
moose.getFieldNames(
'Compartment',
'destFinfo') # returns list of message inlets for a moose element class.
soma.getFieldNames('destFinfo')
moose.showmsg(
'soma') # shows message connetions statistics of the moose element.
model=create_model_sim.setupNeurons(model,network=not net.single)
all_neur_types=model.neurons
#FSIsyn,neuron = cell_proto.neuronclasses(FSI)
#all_neur_types.update(neuron)
population,connections,plas=create_network.create_network(model, net, all_neur_types)
###### Set up stimulation - could be current injection or plasticity protocol
# set num_inject=0 to avoid current injection
if net.num_inject<np.inf :
inject_pop=inject_func.inject_pop(population['pop'],net.num_inject)
else:
inject_pop=population['pop']
#Does setupStim work for network?
#create_model_sim.setupStim(model)
pg=inject_func.setupinj(model, param_sim.injection_delay,param_sim.injection_width,inject_pop)
moose.showmsg(pg)
##############--------------output elements
if net.single:
#fname=model.param_stim.Stimulation.Paradigm.name+'_'+model.param_stim.location.stim_dendrites[0]+'.npz'
#simpath used to set-up simulation dt and hsolver
simpath=['/'+neurotype for neurotype in all_neur_types]
create_model_sim.setupOutput(model)
else: #population of neurons
spiketab,vmtab,plastab,catab=net_output.SpikeTables(model, population['pop'], net.plot_netvm, plas, net.plots_per_neur)
#simpath used to set-up simulation dt and hsolver
simpath=[net.netname]
clocks.assign_clocks(simpath, param_sim.simdt, param_sim.plotdt, param_sim.hsolve,model.param_cond.NAME_SOMA)
if model.synYN and (param_sim.plot_synapse or net.single):
#overwrite plastab above, since it is empty
syntab, plastab, stp_tab=tables.syn_plastabs(connections,model)
print(neuron)
print(soma)
print("l=" + str(soma.length))
print("d=" + str(soma.diameter))
print("Rm=" + str(soma.Rm))
print("Vm=" + str(soma.Vm))
print("Cm=" + str(soma.Cm))
print("Em=" + str(soma.Em))
print("initVm=" + str(soma.initVm))
print(dend)
moose.reinit()
moose.start(0.3)
print(soma.Vm)
soma.inject=1e-9
moose.reinit()
moose.start(0.3)
print(soma.Vm)
soma.inject = 0
def create_pulse(pulsename,pulsedelay,pulsewidth,pulselevel,pulsecomp):
pulse = moose.PulseGen(pulsename)
pulse.delay[0]=pulsedelay
pulse.width[0]=pulsewidth
pulse.level[0]=pulselevel
pulse.level[1]=1e-9
pulse.delay[1]=1e9
moose.connect(pulse,'output',pulsecomp,'injectMsg')
pulse = create_pulse('pulse',0,0,0,soma)
print(moose.showmsg(soma))
chan.tau2 = params['tau2']
chan.Ek = params['Erev']
# Test to check NMDA creation.
moose.le('/cell2/dend')
for key, params in synparams.items():
if key == 'nmda':
chan = moose.NMDAChan('/cell2/dend/' + key)
chan.KMg_A = params['mgparams']['A']
chan.KMg_B = params['mgparams']['B']
chan.CMg = params['mgparams']['conc']
chan.temperature = params['temperature']
chan.extCa = params['extCa']
chan.condFraction = params['condFraction']
else:
chan = moose.SynChan('/cell2/dend/' + key)
chan.Gbar = params['Gbar']
chan.tau1 = params['tau1']
chan.tau2 = params['tau2']
chan.Ek = params['Erev']
m = moose.connect(nmdachan, 'ICaOut', capool, 'current')
capool = moose.CaConc('/cell2/dend/capool')
moose.showfield(capool)
m = moose.connect(capool, 'concOut', nmdachan, 'setIntCa')
moose.showmsg('/cell2')
pfile = "layer2.p"
swcfile = "538ser3sl5-cell1-2-a.CNG.swc"
container1 = "cell1"
container2 = "cell2"
cell1 = moose.loadModel(pfile, container1)
cell2 = moose.loadModel(swcfile, container2)
print("P file:")
moose.le("/cell1")
print("SWC file:")
moose.le("/cell2")
moose.showfield("/cell2/soma")
moose.showfield("/cell2/soma_1_0")
moose.showfield("/cell2/soma_2_0")
moose.showmsg("cell1/soma")
moose.showmsg("cell2/soma")
#import neuron
from neuron import h, gui
print("\n\n\n DOING NEURON NOW! \n\n\n")
soma = h.Section(name="soma")
dir(soma)
soma.insert("pas")
soma.nseg = 3
h.psection(sec=soma)
dend = h.Section(name="dend")
dend.connect(soma, 1)
soma_pulse = u.createPulse(soma, 'rollingWave', pulse_dur, pulse_amp,
pulse_delay, pulse_delay2)
soma_Vm, soma_Iex = u.createDataTables(soma, data, soma_pulse)
dend_Vm, dend_Iex = u.createDataTables(dend, data, soma_pulse)
synchan = moose.SynChan('/neuron/swagginDend/glu')
synchan.Gbar = 1e-8
synchan.tau1 = 2e-3
synchan.tau2 = 2e-3
synchan.Ek = -0.010
msg = moose.connect(dend, 'channel', synchan, 'channel')
sh = moose.SimpleSynHandler('/neuron/swagginDend/glu/synhandler')
moose.connect(sh, 'activationOut', synchan, 'activation')
sh.synapse.num = 1
sh.synapse[0].delay = 1e-3
moose.showmsg(sh)
moose.showmsg(synchan)
moose.showfield(sh.synapse[0])
# the commands above specify and connect the randSpike to a synapse on the
# dendrite
pre_syn = moose.RandSpike('presyn_input')
pre_syn.rate = 10
pre_syn.refractT = 1e-3
sh.synapse.num = 1
sh.synapse[0].delay = 5e-3
moose.connect(pre_syn, 'spikeOut', sh.synapse[0], 'addSpike')
# commands above connect another spike from a pre-synaptic neuron to the
# synapse
pre_syn2 = moose.RandSpike('pre_syn2')
def makeChemProto(name='hydra'):
chem = moose.Neutral('/library/' + name)
compt = moose.CubeMesh('/library/' + name + '/' + name)
A = moose.Pool(compt.path + '/A')
B = moose.Pool(compt.path + '/B')
C = moose.Pool(compt.path + '/C')
D = moose.Pool(compt.path + '/D')
E = moose.Pool(compt.path + '/E')
F = moose.Pool(compt.path + '/F')
Z1 = moose.Pool(compt.path + '/Z1')
Z2 = moose.Pool(compt.path + '/Z2')
#A.diffConst=params['diffA']
#B.diffConst=params['diffB']
Adot = moose.Function(A.path + '/Adot')
Bdot = moose.Function(B.path + '/Bdot')
Cdot = moose.Function(C.path + '/Cdot')
Ddot = moose.Function(D.path + '/Ddot')
Edot = moose.Function(E.path + '/Edot')
Fdot = moose.Function(F.path + '/Fdot')
#Zdot = moose.Function( Z.path + '/Zdot' )
#Adot.expr="x6*(1+x7)*(-x0+(5/(1+x1^3))*(2-x0-x3))"
#Bdot.expr="x6*(1+x7)*(0*x0-x1+(3+2*(x2^3/(1+x1^3)))*(1/(1+x0^3))*(2-x1-x4))"
#Cdot.expr="x6*(1+x7)*(0*x0+0*x1-0*x2+0.1*((0.2+0.3*(x0^3/(0.85^3+x0^3)))-x2^2*(0.2+1*x1^3/(0.85^3+x1^3))))"
Adot.expr = "x6*(1+x7)*(-x0+(4.5/(1+x1^3))*(2-x0-x3))"
Bdot.expr = "x6*(1+x7)*(0*x0-x1+(3+0.5*(x2^3/(1+x1^3)))*(1/(1+x0^3))*(2-x1-x4))"
Cdot.expr = "x6*(1+x7)*(0*x0+0*x1-0*x2+0.5*((0.2+0.3*(x0^3/(0.85^3+x0^3)))-x2^2*(0.2+1*x1^3/(0.85^3+x1^3))))"
#Ddot.expr="(1+x6)*x7*(0*x0+0*x1+0*x2-x3+(5/(1+x4^3))*(2-x0-x3))"
#Edot.expr="(1+x6)*x7*(0*x0+0*x1+0*x2+0*x3-x4+(3+2*(x5^3/(1+x4^3)))*(1/(1+x3^3))*(2-x1-x4))"
#Fdot.expr="(1+x6)*x7*(0*x0+0*x1+0*x2+0*x3+0*x4-0*x5+0.1*((0.2+0.3*(x3^3/(0.85^3+x3^3)))-x5^2*(0.2+1*x4^3/(0.85^3+x4^3))))"
Ddot.expr = "(1+x6)*x7*(0*x0+0*x1+0*x2-x3+(4.5/(1+x4^3))*(2-x0-x3))"
Edot.expr = "(1+x6)*x7*(0*x0+0*x1+0*x2+0*x3-x4+(3+0.5*(x5^3/(1+x4^3)))*(1/(1+x3^3))*(2-x1-x4))"
Fdot.expr = "(1+x6)*x7*(0*x0+0*x1+0*x2+0*x3+0*x4-0*x5+0.5*((0.2+0.3*(x3^3/(0.85^3+x3^3)))-x5^2*(0.2+1*x4^3/(0.85^3+x4^3))))"
print moose.showmsg(Adot)
Adot.x.num = 8 #2
Bdot.x.num = 8 #2
Cdot.x.num = 8 #2
Ddot.x.num = 8 #2
Edot.x.num = 8 #2
Fdot.x.num = 8 #2
#A.nInit=10
#B.nInit=5
moose.connect(A, 'nOut', Adot.x[0], 'input')
moose.connect(B, 'nOut', Adot.x[1], 'input')
moose.connect(C, 'nOut', Adot.x[2], 'input')
moose.connect(D, 'nOut', Adot.x[3], 'input')
moose.connect(E, 'nOut', Adot.x[4], 'input')
moose.connect(F, 'nOut', Adot.x[5], 'input')
moose.connect(Z1, 'nOut', Adot.x[6], 'input')
moose.connect(Z2, 'nOut', Adot.x[7], 'input')
moose.connect(Adot, 'valueOut', A, 'increment')
moose.connect(A, 'nOut', Bdot.x[0], 'input')
moose.connect(B, 'nOut', Bdot.x[1], 'input')
moose.connect(C, 'nOut', Bdot.x[2], 'input')
moose.connect(D, 'nOut', Bdot.x[3], 'input')
moose.connect(E, 'nOut', Bdot.x[4], 'input')
moose.connect(F, 'nOut', Bdot.x[5], 'input')
moose.connect(Z1, 'nOut', Bdot.x[6], 'input')
moose.connect(Z2, 'nOut', Bdot.x[7], 'input')
moose.connect(Bdot, 'valueOut', B, 'increment')
moose.connect(A, 'nOut', Cdot.x[0], 'input')
moose.connect(B, 'nOut', Cdot.x[1], 'input')
moose.connect(C, 'nOut', Cdot.x[2], 'input')
moose.connect(D, 'nOut', Cdot.x[3], 'input')
moose.connect(E, 'nOut', Cdot.x[4], 'input')
moose.connect(F, 'nOut', Cdot.x[5], 'input')
moose.connect(Z1, 'nOut', Cdot.x[6], 'input')
moose.connect(Z2, 'nOut', Cdot.x[7], 'input')
moose.connect(Cdot, 'valueOut', C, 'increment')
moose.connect(A, 'nOut', Ddot.x[0], 'input')
moose.connect(B, 'nOut', Ddot.x[1], 'input')
moose.connect(C, 'nOut', Ddot.x[2], 'input')
moose.connect(D, 'nOut', Ddot.x[3], 'input')
moose.connect(E, 'nOut', Ddot.x[4], 'input')
moose.connect(F, 'nOut', Ddot.x[5], 'input')
moose.connect(Z1, 'nOut', Ddot.x[6], 'input')
moose.connect(Z2, 'nOut', Ddot.x[7], 'input')
moose.connect(Ddot, 'valueOut', D, 'increment')
moose.connect(A, 'nOut', Edot.x[0], 'input')
moose.connect(B, 'nOut', Edot.x[1], 'input')
moose.connect(C, 'nOut', Edot.x[2], 'input')
moose.connect(D, 'nOut', Edot.x[3], 'input')
moose.connect(E, 'nOut', Edot.x[4], 'input')
moose.connect(F, 'nOut', Edot.x[5], 'input')
moose.connect(Z1, 'nOut', Edot.x[6], 'input')
moose.connect(Z2, 'nOut', Edot.x[7], 'input')
moose.connect(Edot, 'valueOut', E, 'increment')
moose.connect(A, 'nOut', Fdot.x[0], 'input')
moose.connect(B, 'nOut', Fdot.x[1], 'input')
moose.connect(C, 'nOut', Fdot.x[2], 'input')
moose.connect(D, 'nOut', Fdot.x[3], 'input')
moose.connect(E, 'nOut', Fdot.x[4], 'input')
moose.connect(F, 'nOut', Fdot.x[5], 'input')
moose.connect(Z1, 'nOut', Fdot.x[6], 'input')
moose.connect(Z2, 'nOut', Fdot.x[7], 'input')
moose.connect(Fdot, 'valueOut', F, 'increment')
return compt
def moose_main(corticalinput):
import numpy as np
import matplotlib.pyplot as plt
# plt.ion()
import moose
from moose_nerp.prototypes import (create_model_sim,
clocks,
inject_func,
create_network,
tables,
net_output)
from moose_nerp import d1opt as model
from moose_nerp import str_net as net
# additional, optional parameter overrides specified from with python terminal
# model.Condset.D1.NaF[model.param_cond.prox] /= 3
# model.Condset.D1.KaS[model.param_cond.prox] *= 3
net.connect_dict['D1']['ampa']['extern1'].dend_loc.postsyn_fraction = 0.8
net.param_net.tt_Ctx_SPN.filename = corticalinput
print('cortical_fraction = {}'.format(net.connect_dict['D1']['ampa']['extern1'].dend_loc.postsyn_fraction))
model.synYN = True
model.plasYN = True
model.calYN = True
model.spineYN = True
net.single = True
create_model_sim.setupOptions(model)
param_sim = model.param_sim
param_sim.useStreamer = True
param_sim.plotdt = .1e-3
param_sim.stim_loc = model.NAME_SOMA
param_sim.stim_paradigm = 'inject'
param_sim.injection_current = [0] # [-0.2e-9, 0.26e-9]
param_sim.injection_delay = 0.2
param_sim.injection_width = 0.4
param_sim.simtime = 21
net.num_inject = 0
net.confile = 'str_connect_plas_simd1opt_{}_corticalfraction_{}'.format(net.param_net.tt_Ctx_SPN.filename, 0.8)
if net.num_inject == 0:
param_sim.injection_current = [0]
#################################-----------create the model: neurons, and synaptic inputs
model = create_model_sim.setupNeurons(model, network=not net.single)
all_neur_types = model.neurons
# FSIsyn,neuron = cell_proto.neuronclasses(FSI)
# all_neur_types.update(neuron)
population, connections, plas = create_network.create_network(model, net, all_neur_types)
###### Set up stimulation - could be current injection or plasticity protocol
# set num_inject=0 to avoid current injection
if net.num_inject < np.inf:
inject_pop = inject_func.inject_pop(population['pop'], net.num_inject)
else:
inject_pop = population['pop']
# Does setupStim work for network?
# create_model_sim.setupStim(model)
pg = inject_func.setupinj(model, param_sim.injection_delay, param_sim.injection_width, inject_pop)
moose.showmsg(pg)
##############--------------output elements
if net.single:
# fname=model.param_stim.Stimulation.Paradigm.name+'_'+model.param_stim.location.stim_dendrites[0]+'.npz'
# simpath used to set-up simulation dt and hsolver
simpath = ['/' + neurotype for neurotype in all_neur_types]
create_model_sim.setupOutput(model)
else: # population of neurons
spiketab, vmtab, plastab, catab = net_output.SpikeTables(model, population['pop'], net.plot_netvm, plas,
net.plots_per_neur)
# simpath used to set-up simulation dt and hsolver
simpath = [net.netname]
clocks.assign_clocks(simpath, param_sim.simdt, param_sim.plotdt, param_sim.hsolve, model.param_cond.NAME_SOMA)
if model.synYN and (param_sim.plot_synapse or net.single):
# overwrite plastab above, since it is empty
syntab, plastab, stp_tab = tables.syn_plastabs(connections, model)
nonstim_plastab = tables.nonstimplastabs(plas)
# Streamer to prevent Tables filling up memory on disk
# This is a hack, should be better implemented
if param_sim.useStreamer == True:
allTables = moose.wildcardFind('/##[ISA=Table]')
streamer = moose.Streamer('/streamer')
streamer.outfile = 'plas_simd1opt_{}_corticalfraction_{}.npy'.format(net.param_net.tt_Ctx_SPN.filename, 0.8)
moose.setClock(streamer.tick, 0.1)
for t in allTables:
if any(s in t.path for s in ['plas', 'VmD1_0', 'extern', 'Shell_0']):
streamer.addTable(t)
else:
t.tick = -2
################### Actually run the simulation
def run_simulation(injection_current, simtime):
print(u'◢◤◢◤◢◤◢◤ injection_current = {} ◢◤◢◤◢◤◢◤'.format(injection_current))
pg.firstLevel = injection_current
moose.reinit()
moose.start(simtime, True)
traces, names = [], []
for inj in param_sim.injection_current:
run_simulation(injection_current=inj, simtime=param_sim.simtime)
weights = [w.value for w in moose.wildcardFind('/##/plas##[TYPE=Function]')]
plt.figure()
plt.hist(weights, bins=100)
plt.title('plas_sim_{}_corticalfraction_{}'.format(net.param_net.tt_Ctx_SPN.filename, cortical_fraction))
plt.savefig('plas_simd1opt_{}_corticalfraction_{}.png'.format(net.param_net.tt_Ctx_SPN.filename, 0.8))
if param_sim.useStreamer == True:
import atexit
atexit.register(moose.quit)
return weights
synchan.Gbar = 1E-8
synchan.tau1 = 2E-3
synchan.tau2 = 2E-3
synchan.Ek = -10E-3
# Connections
moose.connect(soma, 'axialOut', dend, 'handleAxial')
moose.connect(dend, 'channel', synchan, 'channel')
sh = moose.SimpleSynHandler(synchan.path + '/synhandler')
moose.connect(sh, 'activationOut', synchan, 'activation')
sh.synapse.num = 1
sh.synapse[0].delay = 1E-3
moose.showmsg(sh)
presyn = moose.RandSpike('presyn_input')
presyn.rate = 1.3
presyn.refractT = 1E-3
moose.connect(presyn, 'spikeOut', sh.synapse[0], 'addSpike')
sh.synapse.num = 2
sh.synapse[1].delay = 0.1E-3
presyn2 = moose.RandSpike('presyn_input2')
presyn2.rate = 3.5
presyn2.refractT = 1E-3
moose.connect(presyn2, 'spikeOut', sh.synapse[1], 'addSpike')
spiketable1 = moose.Table('spikes1')