Last modified by adavison on 2022/10/04 13:53
From version 27.18
edited by shailesh
on 2021/10/08 11:35
Change comment: There is no comment for this version
To version 27.14
edited by shailesh
on 2021/10/08 11:20
Change comment: There is no comment for this version

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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. 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.
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.
127 127  
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 -
135 135  We start here with the installation of Brian 2. Brian 2 can be installed simply using the pip command.
136 136  
137 137  (% class="box infomessage" %)
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202 202  \\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.
203 203  )))
204 204  
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.
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 on Python.
206 206  
207 207  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:
208 208  
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230 230  \\exit()
231 231  )))
232 232  
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.
234 234  
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:
236 236  
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 -
246 246  (% class="box successmessage" %)
247 247  (((
248 248  **Slide** recap of learning objectives
249 249  )))
250 250  
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.
233 +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.
252 252  
235 +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 +
253 253  (% class="box successmessage" %)
254 254  (((
255 255  **Slide** useful links
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259 259  [[(% style="color:#000000" %)https:~~/~~/neuron.yale.edu/neuron/>>https://neuron.yale.edu/neuron/]]
260 260  )))
261 261  
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.
263 263  
264 264  (% class="box successmessage" %)
265 265  (((