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17	17
18	18	== Format ==
19	19
20		-This tutorial will be a video combining slides, animations, and screencast elements. The intended duration is 10 minutes.
	20	+.
21	21
22	22	== Script ==
23	23
24		-(% class="wikigeneratedid" id="HIntroduceyourself28ifvideo29" %)
25		-(% class="small" %)**Introduce yourself**
	24	+=== Introduce yourself (if video) ===
26	26
27		-Hello, my name is X.
	26	+.
28	28
29		-This video is one of a series of tutorials for PyNN, which is Python software for modelling and simulating spiking neural networks.
	28	+=== State the learning objectives (In this tutorial, you will learn to do X…) ===
30	30
31		-For a list of the other tutorials in this series, you can visit ebrains.eu/service/pynn, that's p-y-n-n.
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32	32
33		-(% class="wikigeneratedid" id="HStatethelearningobjectives28Inthistutorial2CyouwilllearntodoX202629" %)
34		-(% class="small" %)**State the learning objectives**
	32	+=== State prerequisites ===
35	35
36		-In this tutorial, you will learn the basics of PyNN: how to build a simple network of integrate-and-fire neurons using PyNN, how to run simulation experiments with this network using different simulators, and how to visualize the data generated by these experiments.
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37	37
38		-(% class="wikigeneratedid" id="HStateprerequisites" %)
39		-(% class="small" %)**State prerequisites**
	36	+=== Description, explanation, and practice ===
40	40
41		-To follow this tutorial, you need a basic knowledge of neuroscience (high-school level or greater), basic familiarity with the Python programming language, and you should have already followed our earlier tutorial video which guides you through the installation process.
	38	+.
42	42
43		-This video covers PyNN 0.10. If you've installed a more recent version of PyNN, you might want to look for an updated version of this video.
	40	+=== Summary (In this tutorial, you have learned to do X…) ===
44	44
45		-(% class="wikigeneratedid" id="HDescription2Cexplanation2Candpractice" %)
46		-(% class="small" %)**Description, explanation, and practice**
47		-
48		-PyNN is a tool for building models of nervous systems, and parts of nervous systems, at the level of individual neurons and synapses.
49		-
50		-We'll start off creating a group of 100 neurons, using a really simple model of a neuron, the leaky integrate-and-fire model.
51		-
52		-When we inject positive current into this model, either from an electrode or from an excitatory synapse, it increases the voltage across the cell membrane, until the voltage reaches a certain threshold.
53		-
54		-At that point, the neuron produces an action potential, also called a spike, and the membrane voltage is reset.
55		-
56		-Let's start by writing a docstring, "Simple network model using PyNN".
57		-
58		-For now, we're going to use the NEST simulator to simulate this model, so we import the PyNN-for-NEST module.
59		-
60		-Like with any numerical model, we need to break time down into small steps, so let's set that up with steps of 0.1 milliseconds.
61		-
62		-PyNN comes with a selection of integrate-and-fire models. We're going to use the IF_curr_exp model, where "IF" is for integrate-and-fire, "curr" means that synaptic responses are changes in current, and "exp" means that the shape of the current is a decaying exponential function.
63		-
64		-This is where we set the parameters of the model: the resting membrane potential is -65 millivolts, the spike threshold is -55 millivolts, the reset voltage after a spike is again -65 millivolts, the refractory period after a spike is one millisecond, the membrane time constant is 10 milliseconds, and the membrane capacitance is 1 nanofarad. We're also going to inject a constant bias current of 0.1 nanoamps into these neurons, so that we get some action potentials.
65		-
66		-Let's create 100 of these neurons, then we're going to record the membrane voltage, and run a simulation for 100 milliseconds.
67		-
68		-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).
69		-
70		-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.
71		-
72		-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.
73		-
74		-Let's change that. In nature every neuron is a little bit different, so let's set the resting membrane potential and the spike threshold randomly from a Gaussian distribution, and let's plot membrane voltage from _all_ the  neurons.
75		-
76		-Now if we run our simulation again, we can see the effect of this heterogeneity in the neuron population.
77		-
78		-
79		-(% class="wikigeneratedid" id="HSummary28Inthistutorial2CyouhavelearnedtodoX202629" %)
80		-(% class="small" %)**Summary (In this tutorial, you have learned to do X…)**
81		-
82	82	.
83	83
84		-(% class="wikigeneratedid" id="HAcknowledgementsifappropriate" %)
85		-(% class="small" %)**Acknowledgements if appropriate**
	44	+=== Acknowledgements if appropriate ===
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87	87	.
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89		-(% class="wikigeneratedid" id="HReferencestowebsites28Formoreinformation2Cvisitusat202629" %)
90		-(% class="small" %)**References to websites (For more information, visit us at…)**
	48	+=== References to websites (For more information, visit us at…) ===
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94		-(% class="wikigeneratedid" id="HContactinformation28Forquestions2Ccontactusat202629" %)
95		-(% class="small" %)**Contact information (For questions, contact us at…)**
	52	+=== Contact information (For questions, contact us at…) ===
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97	97	.