def generate():
dt = 0.025
simtime = 1000
################################################################################
### Build new network
net = Network(id="Example7_Brunel2000")
net.notes = "Example 7: based on network of Brunel 2000"
net.parameters = {
"g": 4,
"eta": 1,
"order": 5,
"epsilon": 0.1,
"J": 0.1,
"delay": 1.5,
"tauMem": 20.0,
"tauSyn": 0.1,
"tauRef": 2.0,
"U0": 0.0,
"theta": 20.0,
}
cell = Cell(id="ifcell", pynn_cell="IF_curr_alpha")
cell.parameters = {
"tau_m": "tauMem",
"tau_refrac": "tauRef",
"v_rest": "U0",
"v_reset": "U0",
"v_thresh": "theta",
"cm": 0.001,
"i_offset": 0,
}
# cell = Cell(id='hhcell', neuroml2_source_file='test_files/hhcell.cell.nml')
net.cells.append(cell)
poisson_input = Cell(id="poisson_input", pynn_cell="SpikeSourcePoisson")
poisson_input.parameters = {
"rate":
"1000 * (eta*theta/(J*4*order*epsilon*tauMem)) * (4*order*epsilon)",
"start": 0,
"duration": 1e9,
}
net.cells.append(poisson_input)
r1 = RectangularRegion(id="region1",
x=0,
y=0,
z=0,
width=1000,
height=100,
depth=1000)
net.regions.append(r1)
pE = Population(
id="Epop",
size="4*order",
component=cell.id,
properties={
"color": ".9 0 0",
"radius": 5
},
random_layout=RandomLayout(region=r1.id),
)
pEpoisson = Population(
id="expoisson",
size="4*order",
component=poisson_input.id,
properties={
"color": "0.9 0.7 0.7",
"radius": 3
},
random_layout=RandomLayout(region=r1.id),
)
pI = Population(
id="Ipop",
size="1*order",
component=cell.id,
properties={
"color": "0 0 .9",
"radius": 5
},
random_layout=RandomLayout(region=r1.id),
)
pIpoisson = Population(
id="inpoisson",
size="1*order",
component=poisson_input.id,
properties={
"color": "0.7 0.7 0.9",
"radius": 3
},
random_layout=RandomLayout(region=r1.id),
)
net.populations.append(pE)
net.populations.append(pEpoisson)
net.populations.append(pI)
net.populations.append(pIpoisson)
net.synapses.append(
Synapse(
id="ampa",
pynn_receptor_type="excitatory",
pynn_synapse_type="curr_alpha",
parameters={"tau_syn": 0.1},
))
net.synapses.append(
Synapse(
id="gaba",
pynn_receptor_type="inhibitory",
pynn_synapse_type="curr_alpha",
parameters={"tau_syn": 0.1},
))
delay_ext = dt
downscale = 1
J_eff = "J*%s" % (downscale)
# synaptic weights, scaled for alpha functions, such that
# for constant membrane potential, charge J would be deposited
fudge = 0.00041363506632638 # ensures dV = J at V=0
JE = "((%s)/tauSyn)*%s" % (J_eff, fudge)
JI = "-1*g*%s" % (JE)
net.projections.append(
Projection(
id="projEinput",
presynaptic=pEpoisson.id,
postsynaptic=pE.id,
synapse="ampa",
delay=delay_ext,
weight=JE,
one_to_one_connector=OneToOneConnector(),
))
net.projections.append(
Projection(
id="projIinput",
presynaptic=pIpoisson.id,
postsynaptic=pI.id,
synapse="ampa",
delay=delay_ext,
weight=JE,
one_to_one_connector=OneToOneConnector(),
))
net.projections.append(
Projection(
id="projEE",
presynaptic=pE.id,
postsynaptic=pE.id,
synapse="ampa",
delay="delay",
weight=JE,
random_connectivity=RandomConnectivity(probability="epsilon"),
))
net.projections.append(
Projection(
id="projEI",
presynaptic=pE.id,
postsynaptic=pI.id,
synapse="ampa",
delay="delay",
weight=JE,
random_connectivity=RandomConnectivity(probability="epsilon"),
))
net.projections.append(
Projection(
id="projIE",
presynaptic=pI.id,
postsynaptic=pE.id,
synapse="gaba",
delay="delay",
weight=JI,
random_connectivity=RandomConnectivity(probability="epsilon"),
))
net.projections.append(
Projection(
id="projII",
presynaptic=pI.id,
postsynaptic=pI.id,
synapse="gaba",
delay="delay",
weight=JI,
random_connectivity=RandomConnectivity(probability="epsilon"),
))
# print(net)
# print(net.to_json())
new_file = net.to_json_file("%s.json" % net.id)
################################################################################
### Build Simulation object & save as JSON
sim = Simulation(
id="SimExample7",
network=new_file,
duration=simtime,
dt=dt,
seed=123,
record_traces={
pE.id: [0, 1],
pI.id: [0, 1]
},
record_spikes={
pE.id: "*",
pI.id: "*",
pEpoisson.id: [0, 1, 2, 3, 4],
pIpoisson.id: [0, 1, 2, 3, 4],
},
)
sim.to_json_file()
return sim, net
from neuromllite import Network, Cell, InputSource, Population, Synapse
from neuromllite import Projection, RandomConnectivity, Input, Simulation
import sys
################################################################################
### Build new network
net = Network(id="Spikers")
net.notes = "Example with spiking entities.."
net.parameters = {"N": 10, "weightInput": 10, "input_rate": 40}
cell = Cell(id="iafcell", pynn_cell="IF_cond_alpha")
cell.parameters = {"tau_refrac": 10}
net.cells.append(cell)
input_cell = Cell(id="InputCell", pynn_cell="SpikeSourcePoisson")
input_cell.parameters = {
"start": 0,
"duration": 10000000000,
"rate": "input_rate"
}
net.cells.append(input_cell)
input_cell_100 = Cell(id="InputCell100", pynn_cell="SpikeSourcePoisson")
input_cell_100.parameters = {"start": 0, "duration": 10000000000, "rate": 100}
net.cells.append(input_cell_100)
input_source_p0 = InputSource(id="poissonFiringSyn",
neuroml2_source_file="../test_files/inputs.nml")
net.input_sources.append(input_source_p0)
from neuromllite import Projection, RandomConnectivity, Input, Simulation
import sys
################################################################################
### Build new network
net = Network(id='PopExample')
net.notes = 'Testing...'
net.seed = 1234
net.parameters = { 'N': 10, 'fractionE': 0.8, 'weightInput': 1, 'Wei':0.01, 'Wie':0.01}
cell = Cell(id='iafcell', pynn_cell='IF_cond_alpha')
cell.parameters = { "tau_refrac":0}
net.cells.append(cell)
input_source = InputSource(id='poissonFiringSyn100Hz', neuroml2_source_file='inputs.nml')
net.input_sources.append(input_source)
net.input_sources.append(input_source)
pE = Population(id='Epop', size='int(N*fractionE)', component=cell.id, properties={'color':'.7 0 0'})
pI = Population(id='Ipop', size='N - int(N*fractionE)', component=cell.id, properties={'color':'0 0 .7'})
net.populations.append(pE)
net.populations.append(pI)
def generate():
dt = 0.025
simtime = 500
################################################################################
### Build new network
net = Network(id='SpikingEI')
net.notes = 'SpikingEI'
net.parameters = {
'order': 5,
'wee': 8,
'wei': 12,
'wie': -12,
'wii': -3,
'w_scale': 0.001,
'in_rate': 400,
'epsilon': 0.5,
'tauMem': 20.0,
'tauSyn': 0.1,
'tauRef': 2.0
}
cell = Cell(id='ifcell', pynn_cell='IF_curr_alpha')
cell.parameters = {
'tau_m': 'tauMem',
'tau_refrac': 'tauRef',
'v_rest': -70,
'v_reset': -70,
'v_thresh': -50,
'cm': 0.001,
"i_offset": 0
}
#cell = Cell(id='hhcell', neuroml2_source_file='test_files/hhcell.cell.nml')
net.cells.append(cell)
poisson_input = Cell(id='poisson_input', pynn_cell='SpikeSourcePoisson')
poisson_input.parameters = {'rate': 'in_rate', 'start': 0, 'duration': 1e9}
net.cells.append(poisson_input)
r1 = RectangularRegion(id='region1',
x=0,
y=0,
z=0,
width=1000,
height=100,
depth=1000)
net.regions.append(r1)
pE = Population(id='Excitatory',
size='4*order',
component=cell.id,
properties={
'color': '.9 0 0',
'radius': 5
},
random_layout=RandomLayout(region=r1.id))
pEpoisson = Population(id='expoisson',
size='4*order',
component=poisson_input.id,
properties={
'color': '0.9 0.7 0.7',
'radius': 3
},
random_layout=RandomLayout(region=r1.id))
pI = Population(id='Inhibitory',
size='1*order',
component=cell.id,
properties={
'color': '0 0 .9',
'radius': 5
},
random_layout=RandomLayout(region=r1.id))
pIpoisson = Population(id='inpoisson',
size='1*order',
component=poisson_input.id,
properties={
'color': '0.7 0.7 0.9',
'radius': 3
},
random_layout=RandomLayout(region=r1.id))
net.populations.append(pE)
net.populations.append(pEpoisson)
net.populations.append(pI)
net.populations.append(pIpoisson)
net.synapses.append(
Synapse(id='ampa',
pynn_receptor_type='excitatory',
pynn_synapse_type='curr_alpha',
parameters={'tau_syn': 0.1}))
net.synapses.append(
Synapse(id='gaba',
pynn_receptor_type='inhibitory',
pynn_synapse_type='curr_alpha',
parameters={'tau_syn': 0.1}))
delay_ext = dt
net.projections.append(
Projection(id='projEinput',
presynaptic=pEpoisson.id,
postsynaptic=pE.id,
synapse='ampa',
delay=delay_ext,
weight=0.01,
one_to_one_connector=OneToOneConnector()))
net.projections.append(
Projection(id='projIinput',
presynaptic=pIpoisson.id,
postsynaptic=pI.id,
synapse='ampa',
delay=delay_ext,
weight=0.01,
one_to_one_connector=OneToOneConnector()))
net.projections.append(
Projection(
id='projEE',
presynaptic=pE.id,
postsynaptic=pE.id,
synapse='ampa',
delay=delay_ext,
weight='wee * w_scale',
random_connectivity=RandomConnectivity(probability='epsilon')))
net.projections.append(
Projection(
id='projEI',
presynaptic=pE.id,
postsynaptic=pI.id,
synapse='ampa',
delay=delay_ext,
weight='wei * w_scale',
random_connectivity=RandomConnectivity(probability='epsilon')))
net.projections.append(
Projection(
id='projIE',
presynaptic=pI.id,
postsynaptic=pE.id,
synapse='gaba',
delay=delay_ext,
weight='wie * w_scale',
random_connectivity=RandomConnectivity(probability='epsilon')))
net.projections.append(
Projection(
id='projII',
presynaptic=pI.id,
postsynaptic=pI.id,
synapse='gaba',
delay=delay_ext,
weight='wii * w_scale',
random_connectivity=RandomConnectivity(probability='epsilon')))
#print(net)
#print(net.to_json())
new_file = net.to_json_file('%s.json' % net.id)
################################################################################
### Build Simulation object & save as JSON
sim = Simulation(id='SimSpiking',
network=new_file,
duration=simtime,
dt=dt,
seed=123,
recordTraces={
pE.id: '*',
pI.id: '*'
},
recordSpikes={'all': '*'})
sim.to_json_file()
return sim, net
from neuromllite import Network, Cell, InputSource, Population, Synapse
from neuromllite import Projection, RandomConnectivity, Input, Simulation
import sys
################################################################################
### Build new network
net = Network(id='IzhikevichTest')
net.notes = 'Example Izhikevich'
net.parameters = {'N': 1}
cell = Cell(id='izhCell', neuroml2_cell='izhikevich2007Cell')
cell.parameters = {}
params = {'v0':'-60mV', 'C':'100 pF', 'k':'0.7 nS_per_mV', \
'vr':'-60 mV', 'vt':'-40 mV', 'vpeak':'35 mV', \
'a':'0.03 per_ms', 'b':'-2 nS', 'c':'-50 mV', 'd':'100 pA'}
for p in params:
cell.parameters[p] = p
net.parameters[p] = params[p]
net.cells.append(cell)
pop = Population(id='izhPop',
size='1',
component=cell.id,
properties={'color': '.7 0 0'})
net.populations.append(pop)
net.parameters['delay'] = '100ms'
################################################################################
### Build new network
net = Network(id='ArborExample')
net.notes = 'Example for testing Arbor'
net.parameters = {
'v_init': -50,
'input_amp': 0.190,
'input_del': 100,
'input_dur': 800
}
cell = Cell(id='test_arbor_cell', arbor_cell='cable_cell')
cell.parameters = {'v_init': 'v_init', 'radius': 3, 'mechanism': 'hh'}
net.cells.append(cell)
'''
cell2 = Cell(id='testcell2', pynn_cell='IF_cond_alpha')
cell2.parameters = { "tau_refrac":5, "i_offset":-.1 }
net.cells.append(cell2)'''
input_source = InputSource(id='i_clamp',
pynn_input='DCSource',
parameters={
'amplitude': 'input_amp',
'start': 'input_del',
'stop': 'input_del+input_dur'
})
### Build new network
net = Network(id="ArborExample")
net.notes = "Example for testing Arbor"
net.parameters = {
"v_init": -50,
"scale": 3,
"input_amp": 0.01,
"input_del": 50,
"input_dur": 5,
}
cell = Cell(id="test_arbor_cell", arbor_cell="cable_cell")
cell.parameters = {"v_init": "v_init", "radius": 3, "mechanism": "hh"}
net.cells.append(cell)
"""
cell2 = Cell(id='testcell2', pynn_cell='IF_cond_alpha')
cell2.parameters = { "tau_refrac":5, "i_offset":-.1 }
net.cells.append(cell2)"""
input_source = InputSource(
id="i_clamp",
pynn_input="DCSource",
parameters={
"amplitude": "input_amp",
"start": "input_del",
"stop": "input_del+input_dur",
},
def generate():
################################################################################
### Build new network
net = Network(id='Example7_Brunel2000')
net.notes = 'Example 7: based on network of Brunel 2000'
net.parameters = {
'g': 4,
'eta': 1,
'order': 5,
'epsilon': 0.1,
'J': 0.1,
'delay': 1.5,
'tauMem': 20.0,
'tauSyn': 0.1,
'tauRef': 2.0,
'U0': 0.0,
'theta': 20.0
}
cell = Cell(id='ifcell', pynn_cell='IF_curr_alpha')
cell.parameters = {
'tau_m': 'tauMem',
'tau_refrac': 'tauRef',
'v_rest': 'U0',
'v_reset': 'U0',
'v_thresh': 'theta',
'cm': 0.001,
"i_offset": 0
}
#cell = Cell(id='hhcell', neuroml2_source_file='test_files/hhcell.cell.nml')
net.cells.append(cell)
expoisson = Cell(id='expoisson', pynn_cell='SpikeSourcePoisson')
expoisson.parameters = {
'rate':
'1000 * (eta*theta/(J*4*order*epsilon*tauMem)) * (4*order*epsilon)',
'start': 0,
'duration': 1e9
}
net.cells.append(expoisson)
'''
input_source = InputSource(id='iclamp0',
pynn_input='DCSource',
parameters={'amplitude':0.002, 'start':100., 'stop':900.})
input_source = InputSource(id='poissonFiringSyn',
neuroml2_input='poissonFiringSynapse',
parameters={'average_rate':"eta", 'synapse':"ampa", 'spike_target':"./ampa"})
net.input_sources.append(input_source)'''
pE = Population(id='Epop',
size='4*order',
component=cell.id,
properties={'color': '1 0 0'})
pEpoisson = Population(id='Einput',
size='4*order',
component=expoisson.id,
properties={'color': '.5 0 0'})
pI = Population(id='Ipop',
size='1*order',
component=cell.id,
properties={'color': '0 0 1'})
net.populations.append(pE)
net.populations.append(pEpoisson)
net.populations.append(pI)
net.synapses.append(
Synapse(id='ampa',
pynn_receptor_type='excitatory',
pynn_synapse_type='curr_alpha',
parameters={'tau_syn': 0.1}))
net.synapses.append(
Synapse(id='gaba',
pynn_receptor_type='inhibitory',
pynn_synapse_type='curr_alpha',
parameters={'tau_syn': 0.1}))
net.projections.append(
Projection(id='projEinput',
presynaptic=pEpoisson.id,
postsynaptic=pE.id,
synapse='ampa',
delay=2,
weight=0.02,
one_to_one_connector=OneToOneConnector()))
'''
net.projections.append(Projection(id='projEE',
presynaptic=pE.id,
postsynaptic=pE.id,
synapse='ampa',
delay=2,
weight=0.002,
random_connectivity=RandomConnectivity(probability=.5)))'''
net.projections.append(
Projection(id='projEI',
presynaptic=pE.id,
postsynaptic=pI.id,
synapse='ampa',
delay=2,
weight=0.02,
random_connectivity=RandomConnectivity(probability=.5)))
'''
net.projections.append(Projection(id='projIE',
presynaptic=pI.id,
postsynaptic=pE.id,
synapse='gaba',
delay=2,
weight=0.02,
random_connectivity=RandomConnectivity(probability=.5)))
net.inputs.append(Input(id='stim',
input_source=input_source.id,
population=pE.id,
percentage=50))'''
#print(net)
#print(net.to_json())
new_file = net.to_json_file('%s.json' % net.id)
################################################################################
### Build Simulation object & save as JSON
sim = Simulation(id='SimExample7',
network=new_file,
duration='1000',
dt='0.025',
seed=123,
recordTraces={
pE.id: '*',
pI.id: '*'
},
recordSpikes={'all': '*'})
sim.to_json_file()
return sim, net
from neuromllite import Network, Cell, InputSource, Population, Synapse, RectangularRegion, RandomLayout
from neuromllite import Projection, RandomConnectivity, Input, Simulation
import sys
################################################################################
### Build new network
net = Network(id='Example4_PyNN')
net.notes = 'Example 4: a network with PyNN cells & inputs'
net.parameters = {'input_amp': 0.99}
cell = Cell(id='testcell', pynn_cell='IF_cond_alpha')
cell.parameters = {"tau_refrac": 5, "i_offset": .1}
net.cells.append(cell)
cell2 = Cell(id='testcell2', pynn_cell='IF_cond_alpha')
cell2.parameters = {"tau_refrac": 5, "i_offset": -.1}
net.cells.append(cell2)
input_source = InputSource(id='i_clamp',
pynn_input='DCSource',
parameters={
'amplitude': 'input_amp',
'start': 200.,
'stop': 800.
})
net.input_sources.append(input_source)
r1 = RectangularRegion(id='region1',
x=0,
y=0,
from neuromllite import Network, Cell, InputSource, Population, Synapse
from neuromllite import Projection, RandomConnectivity, Input, Simulation
import sys
################################################################################
### Build new network
net = Network(id='Spikers')
net.notes = 'Example with spiking entities..'
net.parameters = { 'N': 10, 'weightInput': 10, 'input_rate': 40}
cell = Cell(id='iafcell', pynn_cell='IF_cond_alpha')
cell.parameters = { "tau_refrac":10 }
net.cells.append(cell)
input_cell = Cell(id='InputCell', pynn_cell='SpikeSourcePoisson')
input_cell.parameters = {
'start': 0,
'duration': 10000000000,
'rate': 'input_rate'
}
net.cells.append(input_cell)
input_cell_100 = Cell(id='InputCell100', pynn_cell='SpikeSourcePoisson')
input_cell_100.parameters = {
'start': 0,
'duration': 10000000000,
'rate': 100
}
net.cells.append(input_cell_100)
def generate():
dt = 0.025
simtime = 1000
################################################################################
### Build new network
net = Network(id='ExampleIF')
net.notes = 'Example with IF'
net.parameters = {
'tauMem': 20.0,
'tauSyn': 0.1,
'tauRef': 2,
'V0': -70,
'theta': -50.0,
'scale': 1,
'in_weight': 0.01,
'in_rate': 50
}
ifcell = Cell(id='ifcell', pynn_cell='IF_curr_alpha')
ifcell.parameters = {
'tau_m': 'tauMem',
'tau_refrac': 'tauRef',
'v_rest': 'V0',
'v_reset': 'V0',
'v_thresh': 'theta',
'cm': 0.001,
"i_offset": 0
}
net.cells.append(ifcell)
poisson_input = Cell(id='poisson_input', pynn_cell='SpikeSourcePoisson')
poisson_input.parameters = {'rate': 'in_rate', 'start': 0, 'duration': 1e9}
net.cells.append(poisson_input)
r1 = RectangularRegion(id='region1',
x=0,
y=0,
z=0,
width=1000,
height=100,
depth=1000)
net.regions.append(r1)
pIF = Population(id='IFpop',
size='1*scale',
component=ifcell.id,
properties={
'color': '.9 0 0',
'radius': 5
},
random_layout=RandomLayout(region=r1.id))
net.populations.append(pIF)
pLNP = Population(id='LNPpop',
size='1*scale',
component=ifcell.id,
properties={
'color': '.9 0.9 0',
'radius': 5
},
random_layout=RandomLayout(region=r1.id))
net.populations.append(pLNP)
pEpoisson = Population(id='expoisson',
size='10',
component=poisson_input.id,
properties={
'color': '0.9 0.7 0.7',
'radius': 3
},
random_layout=RandomLayout(region=r1.id))
net.populations.append(pEpoisson)
net.synapses.append(
Synapse(id='ampa',
pynn_receptor_type='excitatory',
pynn_synapse_type='curr_alpha',
parameters={'tau_syn': 0.1}))
net.projections.append(
Projection(id='proj0',
presynaptic=pEpoisson.id,
postsynaptic=pIF.id,
synapse='ampa',
delay=0,
weight='in_weight',
random_connectivity=RandomConnectivity(probability=0.7)))
net.projections.append(
Projection(id='proj1',
presynaptic=pEpoisson.id,
postsynaptic=pLNP.id,
synapse='ampa',
delay=0,
weight='in_weight',
random_connectivity=RandomConnectivity(probability=0.7)))
#print(net)
#print(net.to_json())
new_file = net.to_json_file('%s.json' % net.id)
################################################################################
### Build Simulation object & save as JSON
sim = Simulation(id='SimExampleIF',
network=new_file,
duration=simtime,
dt=dt,
seed=123,
recordTraces={pIF.id: '*'},
recordSpikes={'all': '*'})
sim.to_json_file()
return sim, net
def generate(ref='Example6_PyNN', add_inputs=True):
################################################################################
### Build new network
net = Network(id=ref,
notes='Another network for PyNN - work in progress...')
net.parameters = {
'N_scaling': 0.005,
'layer_height': 400,
'width': 100,
'depth': 100,
'input_weight': 0.1
}
cell = Cell(id='CorticalCell', pynn_cell='IF_curr_exp')
cell.parameters = {
'cm': 0.25, # nF
'i_offset': 0.0, # nA
'tau_m': 10.0, # ms
'tau_refrac': 2.0, # ms
'v_reset': -65.0, # mV
'v_rest': -65.0, # mV
'v_thresh': -50.0 # mV
}
net.cells.append(cell)
if add_inputs:
input_cell = Cell(id='InputCell', pynn_cell='SpikeSourcePoisson')
input_cell.parameters = {
'start': 0,
'duration': 10000000000,
'rate': 150
}
net.cells.append(input_cell)
e_syn = Synapse(id='ampa',
pynn_receptor_type='excitatory',
pynn_synapse_type='curr_exp',
parameters={'tau_syn': 0.5})
net.synapses.append(e_syn)
i_syn = Synapse(id='gaba',
pynn_receptor_type='inhibitory',
pynn_synapse_type='curr_exp',
parameters={'tau_syn': 0.5})
net.synapses.append(i_syn)
N_full = {
'L23': {
'E': 20683,
'I': 5834
},
'L4': {
'E': 21915,
'I': 5479
},
'L5': {
'E': 4850,
'I': 1065
},
'L6': {
'E': 14395,
'I': 2948
}
}
scale = 0.1
pops = []
input_pops = []
pop_dict = {}
layers = ['L23']
layers = ['L23', 'L4', 'L5', 'L6']
for l in layers:
i = 3 - layers.index(l)
r = RectangularRegion(id=l,
x=0,
y=i * net.parameters['layer_height'],
z=0,
width=net.parameters['width'],
height=net.parameters['layer_height'],
depth=net.parameters['depth'])
net.regions.append(r)
for t in ['E', 'I']:
try:
import opencortex.utils.color as occ
if l == 'L23':
if t == 'E': color = occ.L23_PRINCIPAL_CELL
if t == 'I': color = occ.L23_INTERNEURON
if l == 'L4':
if t == 'E': color = occ.L4_PRINCIPAL_CELL
if t == 'I': color = occ.L4_INTERNEURON
if l == 'L5':
if t == 'E': color = occ.L5_PRINCIPAL_CELL
if t == 'I': color = occ.L5_INTERNEURON
if l == 'L6':
if t == 'E': color = occ.L6_PRINCIPAL_CELL
if t == 'I': color = occ.L6_INTERNEURON
except:
color = '.8 0 0' if t == 'E' else '0 0 1'
pop_id = '%s_%s' % (l, t)
pops.append(pop_id)
ref = 'l%s%s' % (l[1:], t.lower())
exec(
ref +
" = Population(id=pop_id, size='int(%s*N_scaling)'%N_full[l][t], component=cell.id, properties={'color':color, 'type':t})"
)
exec("%s.random_layout = RandomLayout(region = r.id)" % ref)
exec("net.populations.append(%s)" % ref)
exec("pop_dict['%s'] = %s" % (pop_id, ref))
if add_inputs:
color = '.8 .8 .8'
input_id = '%s_%s_input' % (l, t)
input_pops.append(input_id)
input_ref = 'l%s%s_i' % (l[1:], t.lower())
exec(
input_ref +
" = Population(id=input_id, size='int(%s*N_scaling)'%N_full[l][t], component=input_cell.id, properties={'color':color})"
)
exec("%s.random_layout = RandomLayout(region = r.id)" %
input_ref)
exec("net.populations.append(%s)" % input_ref)
#l23i = Population(id='L23_I', size=int(100*scale), component=cell.id, properties={'color':})
#l23ei = Population(id='L23_E_input', size=int(100*scale), component=input_cell.id)
#l23ii = Population(id='L23_I_input', size=int(100*scale), component=input_cell.id)
#net.populations.append(l23e)
#net.populations.append(l23ei)
#net.populations.append(l23i)
#net.populations.append(l23ii)
conn_probs = [
[0.1009, 0.1689, 0.0437, 0.0818, 0.0323, 0., 0.0076, 0.],
[0.1346, 0.1371, 0.0316, 0.0515, 0.0755, 0., 0.0042, 0.],
[0.0077, 0.0059, 0.0497, 0.135, 0.0067, 0.0003, 0.0453, 0.],
[0.0691, 0.0029, 0.0794, 0.1597, 0.0033, 0., 0.1057, 0.],
[0.1004, 0.0622, 0.0505, 0.0057, 0.0831, 0.3726, 0.0204, 0.],
[0.0548, 0.0269, 0.0257, 0.0022, 0.06, 0.3158, 0.0086, 0.],
[0.0156, 0.0066, 0.0211, 0.0166, 0.0572, 0.0197, 0.0396, 0.2252],
[0.0364, 0.001, 0.0034, 0.0005, 0.0277, 0.008, 0.0658, 0.1443]
]
if add_inputs:
for p in pops:
proj = Projection(id='proj_input_%s' % p,
presynaptic='%s_input' % p,
postsynaptic=p,
synapse=e_syn.id,
delay=2,
weight='input_weight')
proj.one_to_one_connector = OneToOneConnector()
net.projections.append(proj)
for pre_i in range(len(pops)):
for post_i in range(len(pops)):
pre = pops[pre_i]
post = pops[post_i]
prob = conn_probs[post_i][pre_i] ####### TODO: check!!!!
weight = 1
syn = e_syn
if prob > 0:
if 'I' in pre:
weight = -1
syn = i_syn
proj = Projection(id='proj_%s_%s' % (pre, post),
presynaptic=pre,
postsynaptic=post,
synapse=syn.id,
delay=1,
weight=weight)
proj.random_connectivity = RandomConnectivity(probability=prob)
net.projections.append(proj)
print(net.to_json())
new_file = net.to_json_file('%s.json' % net.id)
################################################################################
### Build Simulation object & save as JSON
recordTraces = {}
recordSpikes = {}
from neuromllite.utils import evaluate
for p in pops:
forecast_size = evaluate(pop_dict[p].size, net.parameters)
recordTraces[p] = list(range(min(2, forecast_size)))
recordSpikes[p] = '*'
for ip in input_pops:
recordSpikes[ip] = '*'
sim = Simulation(id='Sim%s' % net.id,
network=new_file,
duration='100',
dt='0.025',
seed=1234,
recordTraces=recordTraces,
recordSpikes=recordSpikes)
sim.to_json_file()
return sim, net
def generate():
################################################################################
### Build new network
net = Network(id='RunStims')
net.notes = 'Example with spike producers'
net.parameters = { 'rate': 50,
'rateHz': '50Hz',
'periodms': '20ms'}
ssp = Cell(id='ssp', pynn_cell='SpikeSourcePoisson')
ssp.parameters = { 'rate': 'rate',
'start': 0,
'duration': 1e9}
net.cells.append(ssp)
sspPop = Population(id='sspPop', size=1, component=ssp.id, properties={'color':'.5 0 0'})
net.populations.append(sspPop)
sg = Cell(id='sg', neuroml2_cell='SpikeGenerator')
sg.parameters = { 'period': 'periodms'}
net.cells.append(sg)
sgPop = Population(id='sgPop', size=1, component=sg.id, properties={'color':'.5 0 0'})
net.populations.append(sgPop)
sgp = Cell(id='sgp', neuroml2_cell='spikeGeneratorPoisson')
sgp.parameters = { 'average_rate': 'rateHz'}
net.cells.append(sgp)
sgpPop = Population(id='sgpPop', size=1, component=sgp.id, properties={'color':'.5 0 0'})
net.populations.append(sgpPop)
net.synapses.append(Synapse(id='ampa',
pynn_receptor_type='excitatory',
pynn_synapse_type='curr_alpha',
parameters={'tau_syn':0.1}))
net.synapses.append(Synapse(id='gaba',
pynn_receptor_type='inhibitory',
pynn_synapse_type='curr_alpha',
parameters={'tau_syn':0.1}))
#print(net)
#print(net.to_json())
new_file = net.to_json_file('%s.json'%net.id)
################################################################################
### Build Simulation object & save as JSON
sim = Simulation(id='SimTest',
network=new_file,
duration='10000',
dt='0.025',
seed= 123,
recordTraces={'xxx':'*'},
recordSpikes={'all':'*'})
sim.to_json_file()
return sim, net
'bkg_rate': 9600
}
cell = Cell(id='eifcell', pynn_cell='EIF_cond_alpha_isfa_ista')
nesp = defaultParams.neuron_params_default
cell.parameters = {
'cm': nesp['C_m'] / 1000, # Capacitance of the membrane in nF
'tau_refrac': nesp['t_ref'], # Duration of refractory period in ms.
'v_spike':
0.0, # Spike detection threshold in mV. https://github.com/nest/nest-simulator/blob/master/models/aeif_cond_alpha.cpp
'v_reset': nesp['V_reset'], # Reset value for V_m after a spike. In mV.
'v_rest':
nesp['E_L'], # Resting membrane potential (Leak reversal potential) in mV.
'tau_m': nesp['C_m'] /
nesp['g_L'], # Membrane time constant in ms = cm/tau_m*1000.0, C_m/g_L
'i_offset': nesp['I_e'] / 1000, # Offset current in nA
'a': 0, # Subthreshold adaptation conductance in nS.
'b': 0, # Spike-triggered adaptation in nA
'delta_T':
2, # Slope factor in mV. See https://github.com/nest/nest-simulator/blob/master/models/aeif_cond_alpha.cpp
'tau_w':
144.0, # Adaptation time constant in ms. See https://github.com/nest/nest-simulator/blob/master/models/aeif_cond_alpha.cpp
'v_thresh': nesp['V_th'], # Spike initiation threshold in mV
}
net.cells.append(cell)
ssp_pre = Cell(id='ssp_pre',
pynn_cell='SpikeSourcePoisson',
parameters={
from neuromllite import Projection, RandomConnectivity, Input, Simulation
import sys
################################################################################
### Build new network
net = Network(id='SonataExample')
net.notes = 'Example for testing Sonata'
net.parameters = {'input_amp': 0.190, 'input_del': 100, 'input_dur': 800}
cell = Cell(id='testcell', pynn_cell='IF_cond_alpha')
cell.parameters = {
"i_offset": 0,
"cm": 0.117,
"tau_m": 22.1,
"tau_refrac": 3,
"v_reset": -50,
"v_rest": -78,
"v_thresh": -47
}
net.cells.append(cell)
'''
cell2 = Cell(id='testcell2', pynn_cell='IF_cond_alpha')
cell2.parameters = { "tau_refrac":5, "i_offset":-.1 }
net.cells.append(cell2)'''
input_source = InputSource(id='i_clamp',
pynn_input='DCSource',
parameters={
'amplitude': 'input_amp',
def generate():
dt = 0.025
simtime = 1000
################################################################################
### Build new network
net = Network(id='Example7_Brunel2000')
net.notes = 'Example 7: based on network of Brunel 2000'
net.parameters = { 'g': 4,
'eta': 1,
'order': 5,
'epsilon': 0.1,
'J': 0.1,
'delay': 1.5,
'tauMem': 20.0,
'tauSyn': 0.1,
'tauRef': 2.0,
'U0': 0.0,
'theta': 20.0}
cell = Cell(id='ifcell', pynn_cell='IF_curr_alpha')
cell.parameters = { 'tau_m': 'tauMem',
'tau_refrac': 'tauRef',
'v_rest': 'U0',
'v_reset': 'U0',
'v_thresh': 'theta',
'cm': 0.001,
"i_offset": 0}
#cell = Cell(id='hhcell', neuroml2_source_file='test_files/hhcell.cell.nml')
net.cells.append(cell)
poisson_input = Cell(id='poisson_input', pynn_cell='SpikeSourcePoisson')
poisson_input.parameters = { 'rate': '1000 * (eta*theta/(J*4*order*epsilon*tauMem)) * (4*order*epsilon)',
'start': 0,
'duration': 1e9}
net.cells.append(poisson_input)
r1 = RectangularRegion(id='region1', x=0,y=0,z=0,width=1000,height=100,depth=1000)
net.regions.append(r1)
pE = Population(id='Epop',
size='4*order',
component=cell.id,
properties={'color':'.9 0 0', 'radius':5},
random_layout = RandomLayout(region=r1.id))
pEpoisson = Population(id='expoisson',
size='4*order',
component=poisson_input.id,
properties={'color':'0.9 0.7 0.7', 'radius':3},
random_layout = RandomLayout(region=r1.id))
pI = Population(id='Ipop',
size='1*order',
component=cell.id,
properties={'color':'0 0 .9', 'radius':5},
random_layout = RandomLayout(region=r1.id))
pIpoisson = Population(id='inpoisson',
size='1*order',
component=poisson_input.id,
properties={'color':'0.7 0.7 0.9', 'radius':3},
random_layout = RandomLayout(region=r1.id))
net.populations.append(pE)
net.populations.append(pEpoisson)
net.populations.append(pI)
net.populations.append(pIpoisson)
net.synapses.append(Synapse(id='ampa',
pynn_receptor_type='excitatory',
pynn_synapse_type='curr_alpha',
parameters={'tau_syn':0.1}))
net.synapses.append(Synapse(id='gaba',
pynn_receptor_type='inhibitory',
pynn_synapse_type='curr_alpha',
parameters={'tau_syn':0.1}))
delay_ext = dt
downscale = 1
J_eff = 'J*%s'%(downscale)
# synaptic weights, scaled for alpha functions, such that
# for constant membrane potential, charge J would be deposited
fudge = 0.00041363506632638 # ensures dV = J at V=0
JE = '((%s)/tauSyn)*%s'%(J_eff,fudge)
JI = '-1*g*%s'%(JE)
net.projections.append(Projection(id='projEinput',
presynaptic=pEpoisson.id,
postsynaptic=pE.id,
synapse='ampa',
delay=delay_ext,
weight=JE,
one_to_one_connector=OneToOneConnector()))
net.projections.append(Projection(id='projIinput',
presynaptic=pIpoisson.id,
postsynaptic=pI.id,
synapse='ampa',
delay=delay_ext,
weight=JE,
one_to_one_connector=OneToOneConnector()))
net.projections.append(Projection(id='projEE',
presynaptic=pE.id,
postsynaptic=pE.id,
synapse='ampa',
delay='delay',
weight=JE,
random_connectivity=RandomConnectivity(probability='epsilon')))
net.projections.append(Projection(id='projEI',
presynaptic=pE.id,
postsynaptic=pI.id,
synapse='ampa',
delay='delay',
weight=JE,
random_connectivity=RandomConnectivity(probability='epsilon')))
net.projections.append(Projection(id='projIE',
presynaptic=pI.id,
postsynaptic=pE.id,
synapse='gaba',
delay='delay',
weight=JI,
random_connectivity=RandomConnectivity(probability='epsilon')))
net.projections.append(Projection(id='projII',
presynaptic=pI.id,
postsynaptic=pI.id,
synapse='gaba',
delay='delay',
weight=JI,
random_connectivity=RandomConnectivity(probability='epsilon')))
#print(net)
#print(net.to_json())
new_file = net.to_json_file('%s.json'%net.id)
################################################################################
### Build Simulation object & save as JSON
sim = Simulation(id='SimExample7',
network=new_file,
duration=simtime,
dt=dt,
seed= 123,
recordTraces={pE.id:[0,1],pI.id:[0,1]},
recordSpikes={pE.id:'*', pI.id:'*',pEpoisson.id:[0,1,2,3,4],pIpoisson.id:[0,1,2,3,4]})
sim.to_json_file()
return sim, net
###################### Build the network ######################################
net = Network(id='Joglekar1Network_PyNN')
net.notes = 'Joglekar network: a network with PyNN cells & inputs'
net.parameters = {'scale': 0.01}
######################## Cell #################################################
cellE = Cell(id='excitatory', pynn_cell='IF_curr_alpha')
cellI = Cell(id='inhibitory', pynn_cell='IF_curr_alpha')
cellE.parameters = {
"tau_m": tauE_m,
"cm": cE_m,
"v_rest": Vrest,
"v_reset": Vreset,
"v_thresh": Vt,
"tau_refrac": tauRef,
"i_offset": (VextE / R)
}
cellI.parameters = {
"tau_m": tauI_m,
"cm": cI_m,
"v_rest": Vrest,
"v_reset": Vreset,
"v_thresh": Vt,
"tau_refrac": tauRef,
"i_offset": (VextI / R)
}
def generate(ref="Example6_PyNN", add_inputs=True):
################################################################################
### Build new network
net = Network(id=ref, notes="Another network for PyNN - work in progress...")
net.parameters = {
"N_scaling": 0.005,
"layer_height": 400,
"width": 100,
"depth": 100,
"input_weight": 0.1,
}
cell = Cell(id="CorticalCell", pynn_cell="IF_curr_exp")
cell.parameters = {
"cm": 0.25, # nF
"i_offset": 0.0, # nA
"tau_m": 10.0, # ms
"tau_refrac": 2.0, # ms
"v_reset": -65.0, # mV
"v_rest": -65.0, # mV
"v_thresh": -50.0, # mV
}
net.cells.append(cell)
if add_inputs:
input_cell = Cell(id="InputCell", pynn_cell="SpikeSourcePoisson")
input_cell.parameters = {"start": 0, "duration": 10000000000, "rate": 150}
net.cells.append(input_cell)
e_syn = Synapse(
id="ampa",
pynn_receptor_type="excitatory",
pynn_synapse_type="curr_exp",
parameters={"tau_syn": 0.5},
)
net.synapses.append(e_syn)
i_syn = Synapse(
id="gaba",
pynn_receptor_type="inhibitory",
pynn_synapse_type="curr_exp",
parameters={"tau_syn": 0.5},
)
net.synapses.append(i_syn)
N_full = {
"L23": {"E": 20683, "I": 5834},
"L4": {"E": 21915, "I": 5479},
"L5": {"E": 4850, "I": 1065},
"L6": {"E": 14395, "I": 2948},
}
scale = 0.1
pops = []
input_pops = []
pop_dict = {}
layers = ["L23"]
layers = ["L23", "L4", "L5", "L6"]
for l in layers:
i = 3 - layers.index(l)
r = RectangularRegion(
id=l,
x=0,
y=i * net.parameters["layer_height"],
z=0,
width=net.parameters["width"],
height=net.parameters["layer_height"],
depth=net.parameters["depth"],
)
net.regions.append(r)
for t in ["E", "I"]:
try:
import opencortex.utils.color as occ
if l == "L23":
if t == "E":
color = occ.L23_PRINCIPAL_CELL
if t == "I":
color = occ.L23_INTERNEURON
if l == "L4":
if t == "E":
color = occ.L4_PRINCIPAL_CELL
if t == "I":
color = occ.L4_INTERNEURON
if l == "L5":
if t == "E":
color = occ.L5_PRINCIPAL_CELL
if t == "I":
color = occ.L5_INTERNEURON
if l == "L6":
if t == "E":
color = occ.L6_PRINCIPAL_CELL
if t == "I":
color = occ.L6_INTERNEURON
except:
color = ".8 0 0" if t == "E" else "0 0 1"
pop_id = "%s_%s" % (l, t)
pops.append(pop_id)
ref = "l%s%s" % (l[1:], t.lower())
exec(
ref
+ " = Population(id=pop_id, size='int(%s*N_scaling)'%N_full[l][t], component=cell.id, properties={'color':color, 'type':t})"
)
exec("%s.random_layout = RandomLayout(region = r.id)" % ref)
exec("net.populations.append(%s)" % ref)
exec("pop_dict['%s'] = %s" % (pop_id, ref))
if add_inputs:
color = ".8 .8 .8"
input_id = "%s_%s_input" % (l, t)
input_pops.append(input_id)
input_ref = "l%s%s_i" % (l[1:], t.lower())
exec(
input_ref
+ " = Population(id=input_id, size='int(%s*N_scaling)'%N_full[l][t], component=input_cell.id, properties={'color':color})"
)
exec("%s.random_layout = RandomLayout(region = r.id)" % input_ref)
exec("net.populations.append(%s)" % input_ref)
# l23i = Population(id='L23_I', size=int(100*scale), component=cell.id, properties={'color':})
# l23ei = Population(id='L23_E_input', size=int(100*scale), component=input_cell.id)
# l23ii = Population(id='L23_I_input', size=int(100*scale), component=input_cell.id)
# net.populations.append(l23e)
# net.populations.append(l23ei)
# net.populations.append(l23i)
# net.populations.append(l23ii)
conn_probs = [
[0.1009, 0.1689, 0.0437, 0.0818, 0.0323, 0.0, 0.0076, 0.0],
[0.1346, 0.1371, 0.0316, 0.0515, 0.0755, 0.0, 0.0042, 0.0],
[0.0077, 0.0059, 0.0497, 0.135, 0.0067, 0.0003, 0.0453, 0.0],
[0.0691, 0.0029, 0.0794, 0.1597, 0.0033, 0.0, 0.1057, 0.0],
[0.1004, 0.0622, 0.0505, 0.0057, 0.0831, 0.3726, 0.0204, 0.0],
[0.0548, 0.0269, 0.0257, 0.0022, 0.06, 0.3158, 0.0086, 0.0],
[0.0156, 0.0066, 0.0211, 0.0166, 0.0572, 0.0197, 0.0396, 0.2252],
[0.0364, 0.001, 0.0034, 0.0005, 0.0277, 0.008, 0.0658, 0.1443],
]
if add_inputs:
for p in pops:
proj = Projection(
id="proj_input_%s" % p,
presynaptic="%s_input" % p,
postsynaptic=p,
synapse=e_syn.id,
delay=2,
weight="input_weight",
)
proj.one_to_one_connector = OneToOneConnector()
net.projections.append(proj)
for pre_i in range(len(pops)):
for post_i in range(len(pops)):
pre = pops[pre_i]
post = pops[post_i]
prob = conn_probs[post_i][pre_i] ####### TODO: check!!!!
weight = 1
syn = e_syn
if prob > 0:
if "I" in pre:
weight = -1
syn = i_syn
proj = Projection(
id="proj_%s_%s" % (pre, post),
presynaptic=pre,
postsynaptic=post,
synapse=syn.id,
delay=1,
weight=weight,
)
proj.random_connectivity = RandomConnectivity(probability=prob)
net.projections.append(proj)
print(net.to_json())
new_file = net.to_json_file("%s.json" % net.id)
################################################################################
### Build Simulation object & save as JSON
record_traces = {}
record_spikes = {}
from neuromllite.utils import evaluate
for p in pops:
forecast_size = evaluate(pop_dict[p].size, net.parameters)
record_traces[p] = list(range(min(2, forecast_size)))
record_spikes[p] = "*"
for ip in input_pops:
record_spikes[ip] = "*"
sim = Simulation(
id="Sim%s" % net.id,
network=new_file,
duration="100",
dt="0.025",
seed=1234,
record_traces=record_traces,
record_spikes=record_spikes,
)
sim.to_json_file()
return sim, net