def simulate():
"""
this test duplicates Brette et al 2007 COBA network
Only 100 ms are simulated to save time
The results below are taken from running ModelDB code
"""
#make the net
h('random_stream_offset_ = 500'
) # to match the statement in Brette /commmon/init.hoc
# set as 1000 in Brette /common/ranstream.hoc
net = BretteNet()
#instumentation
recording = nu.SpikeRecorder(net.cell_list())
sc = nu.SimulationController()
#run the simulation
sc.set_fixed_dt(0.1)
#sc.set_nthread(2)
sc.set_v_init(-60)
sc.set_celsius(36)
sc.stdrun(100)
#output the results
net.print_stim()
recording.print_spikes()
print("all done")
nur.draw_raster_plot(recording, display=True)
def simulate_net(stim_percentage=5):
net = COBANet(500, inhibitory=20, ex_con=20, inh_con=50, ampa_gmax=0.008)
# instumentation
recording = nu.SpikeRecorder(net.cell_list())
sc = nu.SimulationController()
# for cell in net.cell_list():
# cell.set_bias(0.1)
# net.cell_list()[0].set_bias(0.1001)
# net.cell_list()[-1].set_bias(0.100003)
# net.cell_list()[5].set_bias(0.100001)
# net.cell_list()[-5].set_bias(0.1000002)
stims = list()
ncstims = list()
num_stim = int(net.NCELL * stim_percentage / 100)
for i in range(num_stim):
stim = h.NetStim(0.5)
stim.interval = 50000 / (num_stim - i)
stim.noise = 0.5
stims.append(stim)
stim.number = 10e12
ncstim = h.NetCon(
stim,
net.cell_list()[int(net.NCELL * i / num_stim)].synlist.object(0))
ncstim.weight[0] = 0.02
ncstim.delay = 0
ncstims.append(ncstim)
tvec = h.Vector()
tvec.record(h._ref_t)
vvec = h.Vector()
vvec.record(net.cell_list()[0].soma(0.5)._ref_v)
# run the simulation
sc.set_fixed_dt(0.1)
sc.set_v_init(-60)
sc.set_celsius(36)
sc.stdrun(60000)
# output the results
# recording.print_spikes()
print("all done")
# plt.plot(tvec, vvec)
# plt.figure()
# recording.save_spikes('baseline.csv')
nur.draw_raster_plot(recording)
nur.draw_raster_plot(read_baseline(), color='r', display=True)
def run(end_time):
sc = nu.SimulationController()
sc.set_fixed_dt(0.1)
sc.set_v_init(-60)
sc.set_celsius(36)
sc.stdrun(end_time)
cell1 = self.cellList[i]
cell1.rs.uniform(0, 1)
for j in range(self.NCELL):
if not (i == j):
nc = cell1.connect2target(self.cellList[j].synlist[1])
nc.delay = 0
nc.weight[0] = self.GABA_GMAX*cell1.rs.repick()
self.ncList.append(nc)
def make_stim(self):
''' get rid of stim on cell 0 '''
pass
if __name__ == '__main__':
h.load_file("stdrun.hoc")
net = IzhNet(ampa_gmax=0.0000125, gaba_gmax=0.0005, noise=0.02)
recording = nu.SpikeRecorder(net.cell_list())
sc = nu.SimulationController()
tvec = h.Vector()
tvec.record(h._ref_t)
vvec = h.Vector()
vvec.record(net.cell_list()[300].soma(0.5)._ref_v)
sc.set_fixed_dt(0.1)
sc.set_v_init(-70)
sc.stdrun(10000)
plt.plot(tvec, vvec)
plt.figure()
nur.draw_raster_plot(recording, display=True)