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1		-XWiki.shailesh
	1	+XWiki.annedevismes

Content

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1	1	== Learning objectives ==
2	2
3		-In this tutorial, you will learn how to install PyNN, together with the Brian 2, NEST and NEURON simulators, on Linux.
	3	+In this tutorial, you will learn how to install PyNN, together with the NEST, NEURON, and Brian 2 simulators, on Linux.
4	4
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37	37	**Slide** listing learning objectives
38	38	)))
39	39
40		-In this tutorial, I will guide you through setting up PyNN, together with the Brian 2, NEST, and NEURON 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.
	40	+In this tutorial, I will guide you through setting up PyNN, together with the NEST, NEURON, and Brian 2 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.
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44	44	**Slide** listing prerequisites
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46	46
47		-I will demonstrate 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 are also not expected to vary significantly for other Linux distributions. In the latter case, you can find information on the Internet about how to carry out the equivalent of the tasks demonstrated here. Also, this tutorial focuses only on Python 3, because Python 2 is no longer supported. It is recommended to use Python version 3.6 or higher. I will be using Python 3.8.10 in this tutorial, because it is the default version provided with Ubuntu 20.04.
	47	+I will demonstrate 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 are also not expected to vary significantly for other Linux distributions. In the latter case, you can find information on the Internet about how to carry out the equivalent of the tasks demonstrated here using Ubuntu OS. Also, this tutorial focuses only on Python 3, because Python 2 has now been deprecated. It is recommended to use Python version 3.6 or higher. I will be using Python 3.8.10 in this tutorial, because it is the default version provided with Ubuntu 20.04.
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69	69	cd pynn_project
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71	71
72		-Next, we will create a virtual environment within this directory. Python 3 provides support for creating virtual environments. To use this, we first install the package named 'python3-venv':
	72	+Next, we will create a virtual environment within this directory. Python 3 provides support for creating virtual environments. Since Python 3.6, the recommended method to create a new virtual environment is as follows.
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76		-**Screencast** - terminal
	76	+**Note**
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79		-sudo apt-get install python3-venv
	78	+
	79	+For older versions of Python 3, you might be required to manually install `python3-venv` package before being able to run the below command. To install, run:
	80	+\\sudo apt-get install python3-venv
	81	+\\More recent versions of Python 3 (e.g., v3.9) already have this pre-installed.
80	80	)))
81	81
82		-And once this is installed, we can create a new virtual environment as follows. We name this
83		-
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86	86	**Screencast** - terminal
87		-
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89		-python3 -m venv pynn_env
	87	+\\(% style="color:#000000" %)python3 -m venv pynn_env
90	90	)))
91	91
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125	125	You might be required to run the above command every time you open a new terminal window. Check that the terminal command prompt indicates the name of your virtual environment to confirm that you have indeed activated it.
126	126	)))
127	127
128		-Before we proceed, let us run the following commands to ensure that our environment is setup as required:
	126	+Now that we have our project's virtual environment setup, we are 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. In this tutorial, we will adopt this approach and begin by installing the simulators. For the purposes of this tutorial, we will demonstrate the installation of Brian2, NEURON, and NEST simulators.
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130		-
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133		-**Screencast** - terminal
134		-\\(% style="color:#000000" %)pip install ~-~-upgrade pip
135		-sudo apt install make
136		-)))
137		-
138		-Now that we have our project's virtual environment setup, we are 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. In this tutorial, we will adopt this approach and begin by installing the simulators. For the purposes of this tutorial, we will demonstrate the installation of Brian2, NEST, and NEURON simulators.
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142	142	**Note:**
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180	180
181	181	We will 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.
182	182
183		-At the time of creating this tutorial, the latest version of NEST is v3.1. This is currently supported by PyNN v0.10, and it is likely that other versions of NEST are potentially 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.
	171	+At the time of creating this tutorial, the latest version of NEST is v3.1. This is currently supported by PyNN v0.10, and it is likely that other versions of NEST will 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.
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196	196	(((
197	197	**Screencast** - terminal
198	198	\\(% style="color:#000000" %)nest
199		-
200		-(% style="color:#000000" %)exit
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202	202
203		-This will display the NEST banner, which mentions the version amongst other info. Here, as we can see, we have now installed NEST v3.1 on our system. Next, let's verify that this is indeed accessible via Python.
	189	+This will display the NEST banner, which mentions the version amongst other info. Here, as we can see, we have now installed NEST v3.1 on our system. Let us next verify that this is indeed accessible via Python.
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219	219	If there are no error messages here, and the import is successful, we have completed installing NEST simulator and are able to load it via Python.
220	220
221		-We next move on to the third simulator, NEURON. Similar to Brian2, the installation for NEURON can be easily done via the 'pip' command. Do note that this method of installation does not auto-enable MPI support, which would be required for running simulations in parallel. Do visit the NEURON website if you wish to install on clusters or HPC machines.
	207	+We next move on to the third simulator, NEURON. The installation for NEURON used to be more complex but can now be easily completed by using the 'pip' command.
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275	275	(% style="color:#000000" %)sim.end()
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278		-This confirms that PyNN has been properly setup and also that it is able to employ Brian 2. To verify that PyNN is also able to communicate with NEST and NEURON simulators, we can do the following:
	264	+This confirms that PyNN has been properly setup and also that it is able to employ Brian 2. To verify that PyNN is also able to communicate with NEURON and NEST simulators, we can do the following:
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300	300	This confirms that all the required software packages have been successfully completed and are functioning as expected.
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302		-As a last step, we will install a Python package named 'matplotlib' that would come in handy in the tutorials ahead.
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306		-**Screencast** - terminal
307		-\\(% style="color:#000000" %)pip install matplotlib
308		-)))
309		-
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312	312	**Slide** recap of learning objectives