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edited by shailesh
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1 -02. Installing PyNN
1 +02. Installing PyNN - Linux
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1 -(% class="box warningmessage" %)
2 -(((
3 -tutorials under development for Linux, Mac OS, Windows, Jupyter Lab.
4 -)))
5 -
6 -
7 7  == Learning objectives ==
8 8  
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.
3 +In this tutorial, you will learn how to install PyNN, together with the NEST, NEURON and Brian 2 simulators, on Linux.
10 10  
11 11  (% class="box infomessage" %)
12 12  (((
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43 43  **Slide** listing learning objectives
44 44  )))
45 45  
46 -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.
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.
47 47  
48 48  (% class="box successmessage" %)
49 49  (((
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102 102  (% class="box infomessage" %)
103 103  (((
104 104  **Screencast** - file explorer
105 -\\(% style="color:#000000" %)<< show directory contents; especially lib/python3.9/site-packages >>
99 +\\(% style="color:#000000" %)<< show directory contents; especially lib/python3.8/site-packages >>
106 106  )))
107 107  
108 108  As you see here, only a limited number of basic packages have currently been installed in this virtual environment. In the steps ahead, we shall install various other packages, and you shall see that these would be reflected here.
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123 123  \\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.
124 124  )))
125 125  
126 -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.
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. In this tutorial, we will adopt this approach and begin by installing the simulators. For the purposes of this tutorial, we shall demonstrate the installation of Brian2, NEURON and NEST simulators.
127 127  
122 +(% class="box errormessage" %)
123 +(((
124 +**Note:**
125 +\\If you have previously already installed NEURON or NEST on your system and are installing PyNN now, then you would require to compile NEURON's NMODL fles and NEST's extensions manually. For more instructions on this, take a look at:
126 +[[(% style="color:#000000" %)http:~~/~~/neuralensemble.org/docs/PyNN/installation.html>>http://neuralensemble.org/docs/PyNN/installation.html]]
127 +)))
128 +
128 128  We start here with the installation of Brian 2. Brian 2 can be installed simply using the pip command.
129 129  
130 130  (% class="box infomessage" %)
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138 138  (% class="box infomessage" %)
139 139  (((
140 140  **Screencast** - file explorer
141 -\\(% style="color:#000000" %)<< show directory contents lib/python3.9/site-packages >>
142 +\\(% style="color:#000000" %)<< show directory contents lib/python3.8/site-packages >>
142 142  )))
143 143  
144 144  To confirm that we have properly installed Brian 2 on our computer, we can test as follows:
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210 210  (% class="box infomessage" %)
211 211  (((
212 212  **Screencast** - terminal
213 -\\(% style="color:#000000" %)nrngui
214 +\\(% style="color:#000000" %)nrniv
214 214  )))
215 215  
216 216  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.
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225 225  
226 226  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.
227 227  
229 +Now that we have installed all the simulators we intend to use, we move on to installing PyNN itself. As PyNN is a Python package, we can install it easily using the 'pip' command:
228 228  
231 +(% class="box infomessage" %)
232 +(((
233 +**Screencast** - terminal
234 +\\(% style="color:#000000" %)pip install PyNN
235 +)))
236 +
237 +(% class="box warningmessage" %)
238 +(((
239 +**Note:**
240 +\\Note that PyNN project is spelt with a captial P, small y, and two captital N. The pip command is case-insensitive, so you may write it differently here. But the Python module, as we shall see ahead, is case-sensitive and is spelt starting with a small P. This is in line with general Python convention, whereby package names start with small alphabets. Thus, while importing PyNN module via Python, it needs to be written as 'pyNN'.
241 +)))
242 +
243 +To verify that PyNN has been successfully installed on our system, and that it is indeed able to communicate with the other simulators that we installed earlier, we can try running:
244 +
245 +(% class="box infomessage" %)
246 +(((
247 +**Screencast** - terminal
248 +
249 +(% style="color:#000000" %)python
250 +\\import pyNN.brian2 as sim
251 +
252 +(% style="color:#000000" %)sim.setup()
253 +
254 +(% style="color:#000000" %)sim.end()
255 +)))
256 +
257 +This confirms that PyNN has been properly setup, and also that is able to employ Brian 2. To verify similary that PyNN is also able to communicate with NEURON and NEST simulators:
258 +
259 +(% class="box infomessage" %)
260 +(((
261 +**Screencast** - terminal
262 +
263 +(% style="color:#000000" %)python
264 +\\import pyNN.nest as sim
265 +
266 +(% style="color:#000000" %)sim.setup()
267 +
268 +(% style="color:#000000" %)sim.end()
269 +
270 +
271 +
272 +(% style="color:#000000" %)import pyNN.neuron as sim
273 +
274 +(% style="color:#000000" %)sim.setup()
275 +
276 +(% style="color:#000000" %)sim.end()
277 +)))
278 +
279 +This confirms that all the required software packages have been successfully completed, and are functioning as expected.
280 +
229 229  (% class="box successmessage" %)
230 230  (((
231 231  **Slide** recap of learning objectives