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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	(((
...	...	@@ -19,17 +19,11 @@
19	19
20	20	== Prerequisites ==
21	21
22		-To follow this tutorial, you will need a computer with [Linux/Mac OS/Windows] and a good network connection. You will need to know how to open the terminal application for your operating system.
	22	+To follow this tutorial, you will need a computer with Linux and a good network connection. You will need to know how to open the terminal application for your operating system.
23	23
24		-
25		-OR
26		-
27		-
28		-To follow this tutorial, you will need an EBRAINS account. You should know how to create and use Jupyter notebooks in the EBRAINS Jupyter Lab.
29		-
30	30	== Format ==
31	31
32		-These tutorials will be screencasts, in which the presenter runs commands in a terminal (or in a Jupyer notebook), and the viewer is expected to follow along. The intended duration is 10 minutes. For the Jupyter version of the tutorial, the final notebook will also be made available.
	26	+These tutorials will be screencasts, in which the presenter runs commands in a terminal, and the viewer is expected to follow along. The intended duration is 10-15 minutes.
33	33
34	34	== Script ==
35	35
...	...	@@ -97,6 +97,12 @@
97	97	\\(% style="color:#000000" %)python3 -m venv pynn_env
98	98	)))
99	99
	94	+(% class="box warningmessage" %)
	95	+(((
	96	+**Note:**
	97	+\\Observe that this command is as 'python3' and not simply 'python'. This is because Ubuntu 20, as default, understands only the former. You can find on the Internet various ways to have 'python' also refer to 'python3', but for the purposes of this tutorial we shall keep things simple and try to work with the bare minimum changes to the system.
	98	+)))
	99	+
100	100	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.
101	101
102	102	(% class="box infomessage" %)
...	...	@@ -117,6 +117,12 @@
117	117
118	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	119
	120	+(% class="box warningmessage" %)
	121	+(((
	122	+**Note:**
	123	+\\You might be required to run the above command every time you open a new terminal window. Do verify that the terminal command prompt indicates the name of your virtual environment to confirm that you have indeed activated it.
	124	+)))
	125	+
120	120	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.
121	121
122	122	We start here with the installation of Brian 2. Brian 2 can be installed simply using the pip command.
...	...	@@ -140,18 +140,23 @@
140	140	(% class="box infomessage" %)
141	141	(((
142	142	**Screencast** - terminal
143		-\\(% style="color:#000000" %)python3
	149	+\\(% style="color:#000000" %)python
144	144	\\import brian2
145	145	\\exit()
146	146	)))
147	147
	154	+(% class="box warningmessage" %)
	155	+(((
	156	+**Note: **
	157	+\\You might remember that earlier in this tutorial we had to use the term 'python3' to run Python on our system. But here, as in the rest of this tutorial, we shall simply write 'python'. This is possible because once we have activated our virtual environment, this environment understands that both 'python' and 'python3' are equivalent.
	158	+)))
	159	+
148	148	If there are no error messages here, and the import is successful, then we have completed installing Brian 2.
149	149
	162	+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.
150	150
151		-We shall now move on to install the NEST simulator. Unlike Brian 2, NEST is not a Python package and therefore its installation is a bit more involved. We shall install the NEST module along with PyNEST, which is a Python interface for controlling the NEST kernel.
	164	+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.
152	152
153		-We first install the NEST module. At the time of creating this tutorial, the lastest version of NEST is 3.1. This is supported by  is currently supported by PyNN, and it is likely that other versions of NEST might have issues when used with the current 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.
154		-
155	155	(% class="box infomessage" %)
156	156	(((
157	157	**Screencast** - terminal
...	...	@@ -160,19 +160,79 @@
160	160	\\sudo apt-get install nest
161	161	)))
162	162
163		-At this point, we have installed the NEST module, but it is still not usable via Python. To do so, we next install PyNEST.
	174	+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 NEST on our computer, we can test as follows:
164	164
	176	+(% class="box infomessage" %)
	177	+(((
	178	+**Screencast** - terminal
	179	+\\(% style="color:#000000" %)nest
	180	+)))
165	165
	182	+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.
166	166
	184	+(% class="box infomessage" %)
	185	+(((
	186	+**Screencast** - terminal
	187	+\\(% style="color:#000000" %)python
	188	+\\import nest
	189	+\\exit()
	190	+)))
	191	+
	192	+(% class="box warningmessage" %)
	193	+(((
	194	+**Note:**
	195	+\\I find that I receive a "no module named nest" error, when trying this right after installing NEST. But it succeeds after a restart. So if you do observe an error, close all programs and restart your computer, and try again. This time it should execute as expected.
	196	+)))
	197	+
	198	+If there are no error messages here, and the import is successful, then we have completed installing NEST simulator, and are able to load it via Python.
	199	+
	200	+We next move on to the third simulator, NEURON. The installation for NEURON used to be more involved previously, but can now be easily completed using the 'pip' command:
	201	+
	202	+(% class="box infomessage" %)
	203	+(((
	204	+**Screencast** - terminal
	205	+\\(% style="color:#000000" %)pip install neuron
	206	+)))
	207	+
	208	+This installs the NEURON simulator on your system. To confirm that we have properly installed NEURON, we can test as follows:
	209	+
	210	+(% class="box infomessage" %)
	211	+(((
	212	+**Screencast** - terminal
	213	+\\(% style="color:#000000" %)nrngui
	214	+)))
	215	+
	216	+This will display the NEURON banner, which mentions the version amongst other info. Here, as we can see, we have now installed NEURON v8.0.0 on our system. Let us next verify that this is indeed accessible via Python.
	217	+
	218	+(% class="box infomessage" %)
	219	+(((
	220	+**Screencast** - terminal
	221	+\\(% style="color:#000000" %)python
	222	+\\from neuron import h
	223	+\\exit()
	224	+)))
	225	+
	226	+If there are no error messages here, and the import is successful, then we have completed installing NEURON simulator, and are able to load it via Python.
	227	+
	228	+
167	167	(% class="box successmessage" %)
168	168	(((
169	169	**Slide** recap of learning objectives
170	170	)))
171	171
172		-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.
	234	+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. Also, 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.
173	173
174		-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.
	236	+(% class="box successmessage" %)
	237	+(((
	238	+**Slide** useful links
	239	+\\[[(% style="color:#000000" %)https:~~/~~/realpython.com/python-virtual-environments-a-primer/>>https://realpython.com/python-virtual-environments-a-primer/]](%%)
	240	+[[(% style="color:#000000" %)https:~~/~~/briansimulator.org/install/>>https://briansimulator.org/install/]](%%)
	241	+[[(% style="color:#000000" %)https:~~/~~/nest-simulator.readthedocs.io/en/v3.1/installation/index.html>>https://nest-simulator.readthedocs.io/en/v3.1/installation/index.html]](%%)
	242	+[[(% style="color:#000000" %)https:~~/~~/neuron.yale.edu/neuron/>>https://neuron.yale.edu/neuron/]]
	243	+)))
175	175
	245	+We have listed here some links that might be of interest to users who wish to find more details about the various softwares employed in this tutorial.
	246	+
176	176	(% class="box successmessage" %)
177	177	(((
178	178	**Slide** acknowledgements, contact information
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183	183
184	184	(% class="wikigeneratedid" %)
185	185	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.
186		-
187		-
188		-(% class="wikigeneratedid" %)
189		-[[https:~~/~~/realpython.com/python-virtual-environments-a-primer/>>https://realpython.com/python-virtual-environments-a-primer/]]
190		-[[https:~~/~~/briansimulator.org/install/>>https://briansimulator.org/install/]]
191		-[[https:~~/~~/nest-simulator.readthedocs.io/en/v3.1/installation/index.html>>https://nest-simulator.readthedocs.io/en/v3.1/installation/index.html]]