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Last modified by adavison on 2022/10/04 13:53
From version 27.9
edited by shailesh
on 2021/10/08 11:06
Change comment: There is no comment for this version
To version 27.18
edited by shailesh
on 2021/10/08 11:35
Change comment: There is no comment for this version

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... ... @@ -91,6 +91,12 @@
91 91  \\(% style="color:#000000" %)python3 -m venv pynn_env
92 92  )))
93 93  
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 +
94 94  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.
95 95  
96 96  (% class="box infomessage" %)
... ... @@ -117,8 +117,15 @@
117 117  \\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.
118 118  )))
119 119  
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.
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. 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.
121 121  
128 +(% class="box errormessage" %)
129 +(((
130 +**Note:**
131 +\\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:
132 +[[(% style="color:#000000" %)http:~~/~~/neuralensemble.org/docs/PyNN/installation.html>>http://neuralensemble.org/docs/PyNN/installation.html]]
133 +)))
134 +
122 122  We start here with the installation of Brian 2. Brian 2 can be installed simply using the pip command.
123 123  
124 124  (% class="box infomessage" %)
... ... @@ -140,11 +140,17 @@
140 140  (% class="box infomessage" %)
141 141  (((
142 142  **Screencast** - terminal
143 -\\(% style="color:#000000" %)python3
156 +\\(% style="color:#000000" %)python
144 144  \\import brian2
145 145  \\exit()
146 146  )))
147 147  
161 +(% class="box warningmessage" %)
162 +(((
163 +**Note: **
164 +\\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.
165 +)))
166 +
148 148  If there are no error messages here, and the import is successful, then we have completed installing Brian 2.
149 149  
150 150  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.
... ... @@ -172,7 +172,7 @@
172 172  (% class="box infomessage" %)
173 173  (((
174 174  **Screencast** - terminal
175 -\\(% style="color:#000000" %)python3
194 +\\(% style="color:#000000" %)python
176 176  \\import nest
177 177  \\exit()
178 178  )))
... ... @@ -183,7 +183,7 @@
183 183  \\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.
184 184  )))
185 185  
186 -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 on Python.
205 +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.
187 187  
188 188  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:
189 189  
... ... @@ -206,22 +206,42 @@
206 206  (% class="box infomessage" %)
207 207  (((
208 208  **Screencast** - terminal
209 -\\(% style="color:#000000" %)python3
228 +\\(% style="color:#000000" %)python
210 210  \\from neuron import h
211 211  \\exit()
212 212  )))
213 213  
233 +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.
214 214  
235 +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:
215 215  
237 +(% class="box infomessage" %)
238 +(((
239 +**Screencast** - terminal
240 +\\(% style="color:#000000" %)pip install 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 +
216 216  (% class="box successmessage" %)
217 217  (((
218 218  **Slide** recap of learning objectives
219 219  )))
220 220  
221 -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.
251 +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.
222 222  
223 -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.
253 +(% class="box successmessage" %)
254 +(((
255 +**Slide** useful links
256 +\\[[(% style="color:#000000" %)https:~~/~~/realpython.com/python-virtual-environments-a-primer/>>https://realpython.com/python-virtual-environments-a-primer/]](%%)
257 +[[(% style="color:#000000" %)https:~~/~~/briansimulator.org/install/>>https://briansimulator.org/install/]](%%)
258 +[[(% 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]](%%)
259 +[[(% style="color:#000000" %)https:~~/~~/neuron.yale.edu/neuron/>>https://neuron.yale.edu/neuron/]]
260 +)))
224 224  
262 +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.
263 +
225 225  (% class="box successmessage" %)
226 226  (((
227 227  **Slide** acknowledgements, contact information
... ... @@ -232,9 +232,3 @@
232 232  
233 233  (% class="wikigeneratedid" %)
234 234  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.
235 -
236 -
237 -(% class="wikigeneratedid" %)
238 -[[https:~~/~~/realpython.com/python-virtual-environments-a-primer/>>https://realpython.com/python-virtual-environments-a-primer/]]
239 -[[https:~~/~~/briansimulator.org/install/>>https://briansimulator.org/install/]]
240 -[[https:~~/~~/nest-simulator.readthedocs.io/en/v3.1/installation/index.html>>https://nest-simulator.readthedocs.io/en/v3.1/installation/index.html]]