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6	6
7	7	== Learning objectives ==
8	8
9		-In this tutorial, you will learn how to install PyNN, together with the NEST, NEURON and Brian2 simulators, on Linux / Mac OS / Windows / in EBRAINS Jupyter Lab.
	9	+In this tutorial, you will learn how to install PyNN, together with the NEST, NEURON and Brian 2 simulators, on Linux / Mac OS / Windows / in EBRAINS Jupyter Lab.
10	10
11	11	(% class="box infomessage" %)
12	12	(((
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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, I will guide you through setting up PyNN, together with the NEST, NEURON and Brian 2 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.
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54	54	(% class="box successmessage" %)
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56	56	**Slide** listing prerequisites
57	57	)))
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.
	59	+I shall be demonstrating the installation on a computer with Ubuntu 20.04 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 3.8.10 in this tutorial, as it is the default version provided with Ubuntu 20.04.
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	61	+(% class="box errormessage" %)
	62	+(((
	63	+**Note:**
	64	+Having multiple versions of Python on your system can produce issues while installing NEST. The method shown below will install NEST for the default version of Python provided by your Ubuntu OS. E.g. for Ubuntu 18.04 this might be Python 3.6.9 and for Ubuntu 20.04 it will likely be 3.8.10. If you wish to associate the NEST installation with a different Python version installed on your system, please refer the NEST installation instructions to do so on their website.
	65	+)))
	66	+
61	61	(% class="box infomessage" %)
62	62	(((
63	63	**Screencast** - terminal
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75	75	cd pynn_project
76	76	)))
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:
	84	+Next we shall create a virtual environment within this directory. Python 3 provides support for creating virtual environments. Since Python 3.6, the recommended method of creating a new virtual environment is as follows:
79	79
	86	+(% class="box errormessage" %)
	87	+(((
	88	+**Note:**
	89	+For older versions of Python 3, you might require to manually install `python3-venv` package before being able to run the below command. To install, run:
	90	+\\sudo apt-get install python3-venv
	91	+\\More recent versions of Python 3 (e.g. v3.9) already have this pre-installed.
	92	+)))
	93	+
80	80	(% class="box infomessage" %)
81	81	(((
82	82	**Screencast** - terminal
83		-\\(% style="color:#000000" %)python -m venv pynn_env
	97	+\\(% style="color:#000000" %)python3 -m venv pynn_env
84	84	)))
85	85
86	86	This will create a sub-directory named 'pynn_env' within our project directory, with several files and sub-directories. Let us take a look at the 'site-packages' directory.
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101	101	\\(% style="color:#000000" %)source pynn_env/bin/activate
102	102	)))
103	103
	118	+Notice how this changes the command prompt to show the name of your virtual environment. In our case, we had named it 'pynn_env', and this is now reflected as a prefix to the command prompt. This confirms that we are now in our new virtual environment.
	119	+
104	104	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.
105	105
106		-We start here with the installation of Brian2.
	122	+We start here with the installation of Brian 2. Brian 2 can be installed simply using the pip command.
107	107
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109	109	(((
110	110	**Screencast** - terminal
111		-
	127	+\\(% style="color:#000000" %)pip install brian2
112	112	)))
113	113
	130	+This will install Brian 2, along with all its dependencies such as 'cython', 'numpy', etc. We can now go back into our virtual environment's 'site-packages' directory to see how it is now populated with all these packages.
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	132	+(% class="box infomessage" %)
	133	+(((
	134	+**Screencast** - file explorer
	135	+\\(% style="color:#000000" %)<< show directory contents lib/python3.9/site-packages >>
	136	+)))
	137	+
	138	+To confirm that we have properly installed Brian 2 on our computer, we can test as follows:
	139	+
	140	+(% class="box infomessage" %)
	141	+(((
	142	+**Screencast** - terminal
	143	+\\(% style="color:#000000" %)python3
	144	+\\import brian2
	145	+\\exit()
	146	+)))
	147	+
	148	+If there are no error messages here, and the import is successful, then we have completed installing Brian 2.
	149	+
	150	+We shall now move on to install the NEST simulator. Unlike Brian 2, NEST is not a Python package and therefore it cannot be installed via the 'pip' command.
	151	+
	152	+At the time of creating this tutorial, the lastest version of NEST is v3.1. This is currently supported by PyNN v0.10, and it is likely that other versions of NEST could potentially be incompatible with this version of PyNN. The installation is done by first adding the PPA repository for NEST and updating apt, followed by the installation of NEST itself.
	153	+
	154	+(% class="box infomessage" %)
	155	+(((
	156	+**Screencast** - terminal
	157	+\\(% style="color:#000000" %)sudo add-apt-repository ppa:nest-simulator/nest
	158	+sudo apt-get update
	159	+\\sudo apt-get install nest
	160	+)))
	161	+
	162	+This installs the NEST module along with PyNEST, which is a Python interface for controlling the NEST kernel. This allows us to use NEST via Python. To confirm that we have properly installed Brian 2 on our computer, we can test as follows:
	163	+
	164	+(% class="box infomessage" %)
	165	+(((
	166	+**Screencast** - terminal
	167	+\\(% style="color:#000000" %)python3
	168	+\\import nest
	169	+\\exit()
	170	+)))
	171	+
	172	+If there are no error messages here, and the import is successful, then we have completed installing NEST simulator.
	173	+
	174	+We next move on to the third simulation, NEURON. The installation for NEURON is a bit more involved.
	175	+
	176	+<< add more >>
	177	+
115	115	(% class="box successmessage" %)
116	116	(((
117	117	**Slide** recap of learning objectives
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135	135
136	136	(% class="wikigeneratedid" %)
137	137	[[https:~~/~~/realpython.com/python-virtual-environments-a-primer/>>https://realpython.com/python-virtual-environments-a-primer/]]
	201	+[[https:~~/~~/briansimulator.org/install/>>https://briansimulator.org/install/]]
	202	+[[https:~~/~~/nest-simulator.readthedocs.io/en/v3.1/installation/index.html>>https://nest-simulator.readthedocs.io/en/v3.1/installation/index.html]]