Changes for page 03. Building and simulating a simple model
Last modified by adavison on 2022/10/04 13:55
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... ... @@ -106,11 +106,36 @@ 106 106 (% style="color:#000000" %)cell_type = sim.IF_curr_exp(v_rest=-65, v_thresh=-55, v_reset=-65, t_refrac=1, tau_m=10, cm=1, i_offset=0.1)(%%) 107 107 (% style="color:#e74c3c" %)population1 = sim.Population(100, cell_type, label="Population 1") 108 108 population1.record("v") 109 -sim.run(100.0) 109 +sim.run(100.0)(%%) 110 +\\**Run script in terminal** 110 110 ))) 111 111 112 112 PyNN has some built-in tools for making simple plots, so let's import those, and plot the membrane voltage of the zeroth neuron in our population (remember Python starts counting at zero). 113 113 115 +(% class="box infomessage" %) 116 +((( 117 +**Screencast** - current state of editor 118 +\\(% style="color:#000000" %)"""Simple network model using PyNN""" 119 +\\import pyNN.nest as sim(%%) 120 +(% style="color:#e74c3c" %)from pyNN.utility.plotting import Figure, Panel(%%) 121 +(% style="color:#000000" %)sim.setup(timestep=0.1)(%%) 122 +(% style="color:#000000" %)cell_type = sim.IF_curr_exp(v_rest=-65, v_thresh=-55, v_reset=-65, t_refrac=1, tau_m=10, cm=1, i_offset=0.1)(%%) 123 +(% style="color:#000000" %)population1 = sim.Population(100, cell_type, label="Population 1") 124 +population1.record("v") 125 +sim.run(100.0)(%%) 126 +(% style="color:#e74c3c" %)data_v = population1.get_data().segments[0].filter(name='v')[0] 127 +Figure( 128 + Panel( 129 + data_v[:, 0], 130 + xticks=True, xlabel="Time (ms)", 131 + yticks=True, ylabel="Membrane potential (mV)" 132 + ), 133 + title="Response of neuron #0", 134 + annotations="Simulated with NEST" 135 +).show()(%%) 136 +\\**Run script in terminal** 137 +))) 138 + 114 114 As you'd expect, the bias current causes the membrane voltage to increase until it reaches threshold~-~--it doesn't increase in a straight line because it's a //leaky// integrate-and-fire neuron~-~--then once it hits the threshold the voltage is reset, and then stays at the same level for a short time~-~--this is the refractory period~-~--before it starts to increase again. 115 115 116 116 Now, all 100 neurons in our population are identical, so if we plotted the first neuron, the second neuron, ..., we'd get the same trace.