Summary

• Page properties (1 modified, 0 added, 0 removed)

Details

Page properties

Content

...	...	@@ -49,80 +49,34 @@
49	49	**Slide** listing learning objectives
50	50	)))
51	51
52		-In this tutorial, I will guide you through setting up PyNN, together with the NEST, NEURON and Brian2 simulators, in a Linux  environment. Note that we have a dedicated version of this tutorial for other environments, such as Mac OS, Windows and EBRAINS Jupyter Lab.
	52	+In this tutorial, we will guide you through setting up PyNN, together with the NEST, NEURON and Brian2 simulators, on a Linux  environment. Note that we have a dedicated version of this tutorial for other environments, such as Mac OS, Windows and EBRAINS Jupyter Lab.
53	53
54		-(% class="box successmessage" %)
55		-(((
56		-**Slide** listing prerequisites
57		-)))
	54	+.
58	58
59		-I shall be demonstrating the installation on a computer with Ubuntu 18.04 OS installed. The steps are likely to remain very similar for other versions of Ubuntu OS, and also not expected to vary significantly for other Linux distributions. In the latter case, you will find on the Internet about how to carry out the equivalent of the tasks demonstrated here using Ubuntu OS. Also, the tutorial will focus only on Python 3, as Python 2 has now been deprecated. It is recommended to use Python version 3.6 or higher. I would be using Python 3.9.7 in this tutorial.
	56	+=== State the learning objectives (In this tutorial, you will learn to do X…) ===
60	60
61		-(% class="box infomessage" %)
62		-(((
63		-**Screencast** - terminal
64		-)))
	58	+.
65	65
66		-We shall make use of virtual environments in this tutorial. This allows multiple Python projects to coexist on the same computer, even when they might have different, and even conflicting, requirements. It helps isolate projects and thereby preventing unrequested changes in others, when any one of them is updated.
	60	+=== State prerequisites ===
67	67
68		-We begin by creating a directory for our project.
	62	+.
69	69
70		-(% class="box infomessage" %)
71		-(((
72		-**Screencast** - terminal
73		-\\(% style="color:#000000" %)cd ~~
74		-mkdir pynn_project
75		-cd pynn_project
76		-)))
	64	+=== Description, explanation, and practice ===
77	77
78		-Next we shall create a virtual environment within this directory. Python 3 provides intrinsic support for creating virtual environments. Since Python 3.6, the recommended method of creating a new virtual environment is as follows:
	66	+.
79	79
80		-(% class="box infomessage" %)
81		-(((
82		-**Screencast** - terminal
83		-\\(% style="color:#000000" %)python -m venv pynn_env
84		-)))
	68	+=== Summary (In this tutorial, you have learned to do X…) ===
85	85
86		-A
	70	+.
87	87
88		-(% class="box infomessage" %)
89		-(((
90		-**Screencast** - file explorer
91		-\\<< show directory contents; especially site-packages >>
92		-)))
	72	+=== Acknowledgements if appropriate ===
93	93
	74	+.
94	94
95		-Now that we have our project's virtual environment setup, we are now ready to install PyNN and other simulators. In general, it is advisable to install the various simulators (especially NEURON and NEST) prior to installing PyNN, because PyNN will then auto compile NEURON's NMODL fles and NEST's extensions during installation. Alternatively, this would need to be done manually as described on the PyNN website. In this tutorial, we will adopt the easier approach and begin by installing the simulators. For the purposes of this tutorial, we shall demonstrate the installation of Brian2, NEURON and NEST simulators.
	76	+=== References to websites (For more information, visit us at…) ===
96	96
97		-We start here with the installation of Brian2.
	78	+.
98	98
99		-(% class="box infomessage" %)
100		-(((
101		-**Screencast** - current state of editor
102		-\\
103		-)))
	80	+=== Contact information (For questions, contact us at…) ===
104	104
105		-
106		-(% class="box successmessage" %)
107		-(((
108		-**Slide** recap of learning objectives
109		-)))
110		-
111		-That is the end of this tutorial, in which I've demonstrated how to install PyNN, and other required simulators, in a Linux system. You are now ready to start modeling! To learn about model development in PyNN, do take a look at our next tutorial.
112		-
113		-Als,  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.
114		-
115		-(% class="box successmessage" %)
116		-(((
117		-**Slide** acknowledgements, contact information
118		-)))
119		-
120		-(% class="wikigeneratedid" %)
121		-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.
122		-
123		-(% class="wikigeneratedid" %)
124		-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.
125		-
126		-
127		-(% class="wikigeneratedid" %)
128		-[[https:~~/~~/realpython.com/python-virtual-environments-a-primer/>>https://realpython.com/python-virtual-environments-a-primer/]]
	82	+.