def create_brain():
# Brain simulation set-up
sim.setup(timestep=0.1,
min_delay=0.1,
max_delay=20.0,
threads=1,
rng_seeds=[1234])
## NEURONS ##
# Neuronal parameters
NEURONPARAMS = {
'cm': 0.025,
'v_rest': -60.5,
'tau_m': 10.,
'e_rev_E': 0.0,
'e_rev_I': -75.0,
'v_reset': -60.5,
'v_thresh': -60.0,
'tau_refrac': 10.0,
'tau_syn_E': 2.5,
'tau_syn_I': 2.5
}
# Build the neuronal model
cell_class = sim.IF_cond_alpha(**NEURONPARAMS)
# Define the neuronal population
population = sim.Population(size=4, cellclass=cell_class)
## SYNAPSES ##
# Build the weights matrix
weights = np.zeros((2, 2))
weights[0, 1] = 1.
weights[1, 0] = 1.
weights *= 5e-5
# Synaptic parameters
SYNAPSE_PARAMS = {
"weight": weights,
"delay": 1.0,
'U': 1.0,
'tau_rec': 1.0,
'tau_facil': 1.0
}
# Build synaptic model
synapse_type = sim.TsodyksMarkramSynapse(**SYNAPSE_PARAMS)
## NETWORK ##
# Connect neurons
connector = sim.AllToAllConnector()
sim.Projection(presynaptic_population=population[0:2],
postsynaptic_population=population[2:4],
connector=connector,
synapse_type=synapse_type,
receptor_type='excitatory')
# Initialize the network
sim.initialize(population, v=population.get('v_rest'))
return population
def create_brain():
"""
Initializes PyNN with the minimal neuronal network
"""
sim.setup(timestep=0.1,
min_delay=0.1,
max_delay=20.0,
threads=1,
rng_seeds=[1234])
# Following parameters were taken from the husky braitenberg brain experiment (braitenberg.py)
SENSORPARAMS = {
'cm': 0.025,
'v_rest': -60.5,
'tau_m': 10.,
'e_rev_E': 0.0,
'e_rev_I': -75.0,
'v_reset': -60.5,
'v_thresh': -60.0,
'tau_refrac': 10.0,
'tau_syn_E': 2.5,
'tau_syn_I': 2.5
}
SYNAPSE_PARAMS = {
"weight": 0.5e-4,
"delay": 20.0,
'U': 1.0,
'tau_rec': 1.0,
'tau_facil': 1.0
}
cell_class = sim.IF_cond_alpha(**SENSORPARAMS)
# Define the network structure: 2 neurons (1 sensor and 1 actors)
population = sim.Population(size=2, cellclass=cell_class)
synapse_type = sim.TsodyksMarkramSynapse(**SYNAPSE_PARAMS)
connector = sim.AllToAllConnector()
# Connect neurons
sim.Projection(presynaptic_population=population[0:1],
postsynaptic_population=population[1:2],
connector=connector,
synapse_type=synapse_type,
receptor_type='excitatory')
sim.initialize(population, v=population.get('v_rest'))
return population
def create_brain(dna=l):
"""
Initializes PyNN with the neuronal network that has to be simulated
"""
NEURONPARAMS = {
'v_rest': -60.5,
'tau_m': 4.0,
'tau_refrac': 2.0,
'tau_syn_E': 10.0,
'tau_syn_I': 10.0,
'v_thresh': -60.4,
'v_reset': -60.5
}
SYNAPSE_PARAMS = {"weight": 1.0, "delay": 2.0}
population = sim.Population(10, sim.IF_cond_alpha())
population[0:10].set(**NEURONPARAMS)
# Connect neurons
CIRCUIT = population
SYN = sim.StaticSynapse(**SYNAPSE_PARAMS)
row_counter = 0
for row in dna:
logger.info(row)
n = np.array(row)
for i in range(1, 11):
if n[i] == 1:
r_type = 'excitatory' if dna[i - 1][0] else 'inhibitory'
logger.info('Synapse from Neuron: ' + str(i) + ' to ' +
str(row_counter + 1) + ' ' + r_type)
sim.Projection(
presynaptic_population=CIRCUIT[row_counter:row_counter +
1],
postsynaptic_population=CIRCUIT[i - 1:i],
connector=sim.OneToOneConnector(),
synapse_type=SYN,
receptor_type=r_type)
row_counter += 1
sim.initialize(population, v=population.get('v_rest'))
logger.debug("Circuit description: " + str(population.describe()))
return population
def create_brain():
"""
Initializes PyNN with the minimal neuronal network
"""
#sim.setup(timestep=0.1, min_delay=0.1, max_delay=20., threads=1, rng_seeds=[1234])
## PARAMETER
# neuron setup
n_refl = 100 # amount of reflex neurons
n_raphe = 100 # amount of Raphe neuros per pool
n_total = n_refl + 2 * n_raphe
w = 1.0 # neuron weight
# neuron and synapse parameter
SENSORPARAMS = {
'v_rest': -70.0,
'tau_m': 10.0,
'v_thresh': -50.0,
'tau_refrac': 5.0
}
REFL_PARAMS = {
'cm': 0.025,
'tau_m': 10.0,
'v_reset': -60.0,
'v_thresh': -55.0
}
RAPHENUCLEI_PARAMS = {'cm': 0.025, 'v_reset': -60.0, 'v_thresh': -55.0}
SYNAPSE_PARAMS = {
'weight': w,
'delay': 0.0,
'U': 1.0,
'tau_rec': 1.0,
'tau_facil': 1.0
}
refl_class = sim.IF_cond_alpha(**SENSORPARAMS)
neurons = sim.Population(size=n_total,
cellclass=refl_class,
label='neurons')
sim.initialize(neurons)
return neurons
def create_brain():
NEURONPARAMS = {'v_rest': -60.5,
'tau_m': 4.0,
'tau_refrac': 2.0,
'tau_syn_E': 10.0,
'tau_syn_I': 10.0,
'e_rev_E': 0.0,
'e_rev_I': -75.0,
'v_thresh': -60.4,
'v_reset': -60.5}
SYNAPSE_PARAMS = {"weight": 1.0,
"delay": 2.0}
population = sim.Population(10, sim.IF_cond_alpha())
population[0:10].set(**NEURONPARAMS)
# Connect neurons
CIRCUIT = population
SYN = sim.StaticSynapse(**SYNAPSE_PARAMS)
row_counter = 0
for row in dna:
logger.info(row)
n = np.array(row)
r_type = 'excitatory'
if n[0] == 0:
r_type = 'inhibitory'
for i in range(19, 29):
if n[i] == 1:
sim.Projection(presynaptic_population=CIRCUIT[row_counter:1 + row_counter],
postsynaptic_population=CIRCUIT[i - 19:i - 18],
connector=sim.OneToOneConnector(), synapse_type=SYN,
receptor_type=r_type)
row_counter += 1
sim.initialize(population, v=population.get('v_rest'))
logger.debug("Circuit description: " + str(population.describe()))
return population
def create_brain():
"""
Initializes PyNN with the neuronal network that has to be simulated
"""
SENSORPARAMS = {'v_rest': -60.5,
'cm': 0.025,
'tau_m': 10.,
'tau_refrac': 10.0,
'tau_syn_E': 2.5,
'tau_syn_I': 2.5,
'e_rev_E': 0.0,
'e_rev_I': -75.0,
'v_thresh': -60.0,
'v_reset': -60.5}
GO_ON_PARAMS = {'v_rest': -60.5,
'cm': 0.025,
'tau_m': 10.0,
'e_rev_E': 0.0,
'e_rev_I': -75.0,
'v_reset': -61.6,
'v_thresh': -60.51,
'tau_refrac': 10.0,
'tau_syn_E': 2.5,
'tau_syn_I': 2.5}
# POPULATION_PARAMS = SENSORPARAMS * 5 + GO_ON_PARAMS + SENSORPARAMS * 2
population = sim.Population(8, sim.IF_cond_alpha())
population[0:5].set(**SENSORPARAMS)
population[5:6].set(**GO_ON_PARAMS)
population[6:8].set(**SENSORPARAMS)
# Shared Synapse Parameters
syn_params = {'U': 1.0, 'tau_rec': 1.0, 'tau_facil': 1.0}
# Synaptic weights
WEIGHT_RED_TO_ACTOR = 1.5e-4
WEIGHT_RED_TO_GO_ON = 1.2e-3 # or -1.2e-3?
WEIGHT_GREEN_BLUE_TO_ACTOR = 1.05e-4
WEIGHT_GO_ON_TO_RIGHT_ACTOR = 1.4e-4
DELAY = 0.1
# Connect neurons
CIRCUIT = population
SYN = sim.TsodyksMarkramSynapse(weight=abs(WEIGHT_RED_TO_ACTOR),
delay=DELAY, **syn_params)
sim.Projection(presynaptic_population=CIRCUIT[2:3],
postsynaptic_population=CIRCUIT[7:8],
connector=sim.AllToAllConnector(),
synapse_type=SYN,
receptor_type='excitatory')
sim.Projection(presynaptic_population=CIRCUIT[3:4],
postsynaptic_population=CIRCUIT[6:7],
connector=sim.AllToAllConnector(),
synapse_type=SYN,
receptor_type='excitatory')
SYN = sim.TsodyksMarkramSynapse(weight=abs(WEIGHT_RED_TO_GO_ON),
delay=DELAY, **syn_params)
sim.Projection(presynaptic_population=CIRCUIT[0:2],
postsynaptic_population=CIRCUIT[5:6],
connector=sim.AllToAllConnector(),
synapse_type=SYN,
receptor_type='inhibitory')
SYN = sim.TsodyksMarkramSynapse(weight=abs(WEIGHT_GREEN_BLUE_TO_ACTOR),
delay=DELAY, **syn_params)
sim.Projection(presynaptic_population=CIRCUIT[4:5],
postsynaptic_population=CIRCUIT[7:8],
connector=sim.AllToAllConnector(),
synapse_type=SYN,
receptor_type='excitatory')
SYN = sim.TsodyksMarkramSynapse(weight=abs(WEIGHT_GO_ON_TO_RIGHT_ACTOR),
delay=DELAY, **syn_params)
sim.Projection(presynaptic_population=CIRCUIT[5:6],
postsynaptic_population=CIRCUIT[7:8],
connector=sim.AllToAllConnector(),
synapse_type=SYN,
receptor_type='excitatory')
sim.initialize(population, v=population.get('v_rest'))
logger.info("Circuit description: " + str(population.describe()))
return population
def create_brain():
"""
Initializes PyNN with the minimal neuronal network
"""
#sim.setup(timestep=0.1, min_delay=0.1, max_delay=20.0, threads=1, rng_seeds=[1234])
## PARAMETER
# neuron setup
#n_sens = 10 # amount of sensory neurons (per joint)
n_refl = 100 # amount of reflex neurons
n_raphe = 100
n_test = 100
n_total = n_refl + 2 * n_raphe
w = 1.0 # neuron weight
# neuron and synapse parameter
SENSORPARAMS = {
'cm': 0.025,
'v_rest': -60.5,
'tau_m': 10.,
'e_rev_E': 0.0,
'e_rev_I': -75.0,
'v_reset': -60.5,
'v_thresh': -60.0
}
REFL_PARAMS = {
'cm': 0.025,
'tau_m': 10.0,
'v_reset': -60.0,
'v_thresh': -55.0
}
RAPHENUCLEI_PARAMS = {'cm': 0.025, 'v_reset': -60.0, 'v_thresh': -55.0}
SYNAPSE_PARAMS = {
'weight': w,
'delay': 0.0,
'U': 1.0,
'tau_rec': 1.0,
'tau_facil': 1.0
}
# ask PHILIPP which kind of neurons from PyNN
refl_class = sim.IF_cond_alpha(**SENSORPARAMS)
neurons = sim.Population(size=n_total,
cellclass=refl_class,
label='neurons')
#neurons[0:n_refl].set(**REFL_PARAMS)
#neurons[n_refl:n_total].set(**RAPHENUCLEI_PARAMS)
#sim.Projection(presynaptic_population=pop_j1,
# postsynaptic_population=pop_refl,
# connector=connector,
# synapse_type=synapse_type,
# receptor_type='excitatory')
#poisson_class = sim.SpikeSourcePoisson()
#test_pop = sim.Population(size=n_test, cellclass=poisson_class, label='test_pop')
#test_pop2= sim.Population(size=1, cellclass=refl_class, label='test_pop2')
#test_pop.rate = 1000000.0
#sim.Projection(test_pop, test_pop2, connector = sim.AllToAllConnector())
#population = sim.Assembly(neurons, test_pop, test_pop2)
#sim.initialize(population)
#return population
sim.initialize(neurons)
return neurons