Last modified by adavison on 2022/10/04 13:53
From version 27.10
edited by shailesh
on 2021/10/08 11:16
Change comment: There is no comment for this version
To version 27.6
edited by shailesh
on 2021/10/08 10:36
Change comment: There is no comment for this version

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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 -
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" %)
... ... @@ -146,17 +146,11 @@
146 146  (% class="box infomessage" %)
147 147  (((
148 148  **Screencast** - terminal
149 -\\(% style="color:#000000" %)python
143 +\\(% style="color:#000000" %)python3
150 150  \\import brian2
151 151  \\exit()
152 152  )))
153 153  
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 -
160 160  If there are no error messages here, and the import is successful, then we have completed installing Brian 2.
161 161  
162 162  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.
... ... @@ -184,7 +184,7 @@
184 184  (% class="box infomessage" %)
185 185  (((
186 186  **Screencast** - terminal
187 -\\(% style="color:#000000" %)python
175 +\\(% style="color:#000000" %)python3
188 188  \\import nest
189 189  \\exit()
190 190  )))
... ... @@ -192,39 +192,15 @@
192 192  (% class="box warningmessage" %)
193 193  (((
194 194  **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.
183 +\\I find that I receive a "no module named nest" error, when trying the above 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.
196 196  )))
197 197  
198 198  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.
199 199  
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:
188 +We next move on to the third simulation, NEURON. The installation for NEURON is a bit more involved.
201 201  
202 -(% class="box infomessage" %)
203 -(((
204 -**Screencast** - terminal
205 -\\(% style="color:#000000" %)pip install neuron
206 -)))
190 +<< add more >>
207 207  
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 -
227 -
228 228  (% class="box successmessage" %)
229 229  (((
230 230  **Slide** recap of learning objectives