Changes for page 03. Building and simulating a simple model
Last modified by adavison on 2022/10/04 13:55
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... ... @@ -334,40 +334,96 @@ 334 334 population2.set(i_offset=0) 335 335 population1.record("v") 336 336 population2.record("v")(%%) 337 -(% style="color:# e74c3c" %)connection_algorithm = sim.FixedProbabilityConnector(p=0.5)337 +(% style="color:#000000" %)connection_algorithm = sim.FixedProbabilityConnector(p=0.5) 338 338 synapse_type = sim.StaticSynapse(weight=0.5, delay=0.5) 339 339 connections = sim.Projection(population1, population2, connection_algorithm, synapse_type)(%%) 340 340 (% style="color:#000000" %)sim.run(100.0)(%%) 341 -(% style="color:#000000" %)data_v = population1.get_data().segments[0].filter(name='v')[0] 342 -Figure( 341 +(% style="color:#e74c3c" %)data1_v(% style="color:#000000" %) = population1.get_data().segments[0].filter(name='v')[0](%%) 342 +(% style="color:#e74c3c" %)data2_v = population2.get_data().segments[0].filter(name='v')[0](%%) 343 +(% style="color:#000000" %)Figure( 343 343 Panel( 344 - data_v[:, 0:5], 345 + (% style="color:#e74c3c" %)data1_v(% style="color:#000000" %)[:, 0:5], 346 + xticks=True, (% style="color:#e74c3c" %)--xlabel="Time (ms)",--(%%) 347 +(% style="color:#000000" %) yticks=True, ylabel="Membrane potential (mV)" 348 + ), 349 + (% style="color:#e74c3c" %)Panel( 350 + data2_v[:, 0:5], 345 345 xticks=True, xlabel="Time (ms)", 352 + yticks=True" 353 + ),(%%) 354 +(% style="color:#000000" %) title="Response of (% style="color:#e74c3c" %)simple network(% style="color:#000000" %)", 355 + annotations="Simulated with NEST" 356 +).show() 357 + 358 +**Run script in terminal, show figure** 359 +))) 360 + 361 +(% class="wikigeneratedid" %) 362 +and there we have it, our simple neuronal network of integrate-and-fire neurons, written in PyNN, simulated with NEST. If you prefer to use the NEURON simulator, PyNN makes this very simple, we import the PyNN-for-NEURON module instead. 363 + 364 +(% class="box infomessage" %) 365 +((( 366 +**Screencast** - current state of editor 367 +\\(% style="color:#000000" %)"""Simple network model using PyNN""" 368 +\\import pyNN.(% style="color:#e74c3c" %)neuron(% style="color:#000000" %) as sim(%%) 369 +(% style="color:#000000" %)from pyNN.utility.plotting import Figure, Panel(%%) 370 +(% style="color:#000000" %)from pyNN.random import RandomDistribution(%%) 371 +(% style="color:#000000" %)sim.setup(timestep=0.1)(%%) 372 +(% style="color:#000000" %)cell_type = sim.IF_curr_exp( 373 + (% style="color:#e74c3c" %) (% style="color:#000000" %)v_rest=RandomDistribution('normal', {'mu': -65.0, 'sigma': 1.0}), 374 + v_thresh=RandomDistribution('normal', {'mu': -55.0, 'sigma': 1.0}), 375 + v_reset=RandomDistribution('normal', {'mu': -65.0, 'sigma': 1.0}), (%%) 376 +(% style="color:#000000" %) t_refrac=1, tau_m=10, cm=1, i_offset=0.1)(%%) 377 +(% style="color:#000000" %)population1 = sim.Population(100, cell_type, label="Population 1")(%%) 378 +(% style="color:#000000" %)population2 = sim.Population(100, cell_type, label="Population 2") 379 +population2.set(i_offset=0) 380 +population1.record("v") 381 +population2.record("v")(%%) 382 +(% style="color:#000000" %)connection_algorithm = sim.FixedProbabilityConnector(p=0.5) 383 +synapse_type = sim.StaticSynapse(weight=0.5, delay=0.5) 384 +connections = sim.Projection(population1, population2, connection_algorithm, synapse_type)(%%) 385 +(% style="color:#000000" %)sim.run(100.0)(%%) 386 +(% style="color:#000000" %)data1_v = population1.get_data().segments[0].filter(name='v')[0] 387 +data2_v = population2.get_data().segments[0].filter(name='v')[0] 388 +Figure( 389 + Panel( 390 + data1_v[:, 0:5], 391 + xticks=True, 346 346 yticks=True, ylabel="Membrane potential (mV)" 347 347 ), 348 - title="Response of first five neurons with heterogeneous parameters", 349 - annotations="Simulated with NEST" 394 + Panel( 395 + data2_v[:, 0:5], 396 + xticks=True, xlabel="Time (ms)", 397 + yticks=True" 398 + ),(%%) 399 +(% style="color:#000000" %) title="Response of simple network", 400 + annotations="Simulated with (% style="color:#e74c3c" %)NEURON(% style="color:#000000" %)" 350 350 ).show() 351 351 352 -Run script in terminal, show figure 403 +**Run script in terminal, show figure** 353 353 ))) 354 354 355 -(% class="wikigeneratedid" id="HSummary28Inthistutorial2CyouhavelearnedtodoX202629"%)356 - (% class="small"%)**Summary(Inthis tutorial,youhavelearnedtodoX…)**406 +(% class="wikigeneratedid" %) 407 +As you would hope, NEST and NEURON give essentially identical results. 357 357 358 -. 409 +(% class="box successmessage" %) 410 +((( 411 +**Slide** recap of learning objectives 412 +))) 359 359 360 -(% class="wikigeneratedid" id="HAcknowledgementsifappropriate" %) 361 -(% class="small" %)**Acknowledgements if appropriate** 414 +That is the end of this tutorial, in which I've demonstrated how to build a simple network using PyNN, and to simulate it using two different simulators, NEST and NEURON. 362 362 363 -. 416 +Of course, PyNN allows you to create much more complex networks than this, with more realistic neuron models, synaptic plasticity, spatial structure, and so on. You can also use other simulators, such as Brian or SpiNNaker, and you can run simulations in parallel on clusters or supercomputers. 364 364 365 -(% class="wikigeneratedid" id="HReferencestowebsites28Formoreinformation2Cvisitusat202629" %) 366 -(% class="small" %)**References to websites (For more information, visit us at…)** 418 +We will be releasing a series of tutorials, throughout the rest of 2021 and 2022, to introduce these more advanced features of PyNN, so keep an eye on the EBRAINS website. 367 367 368 -. 420 +(% class="box successmessage" %) 421 +((( 422 +**Slide** acknowledgements, contact information 423 +))) 369 369 370 -(% class="wikigeneratedid" id="HContactinformation28Forquestions2Ccontactusat202629"%)371 - (%class="small"%)**Contact information(Forquestions,contactusat…)**425 +(% class="wikigeneratedid" %) 426 +PyNN has been developed by many different people, with financial support from several different organisations. I'd like to mention in particular the CNRS and the European Commission, through the FACETS, BrainScaleS and Human Brain Project grants. 372 372 373 -. 428 +(% class="wikigeneratedid" %) 429 +For more information visit neuralensemble.org/PyNN. If you have questions you can contact us through the PyNN Github project, the NeuralEnsemble forum, EBRAINS support, or the EBRAINS Community.