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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 27.2
edited by shailesh
on 2021/10/08 10:23
Change comment: There is no comment for this version

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... ... @@ -91,12 +91,6 @@
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" %)
... ... @@ -117,12 +117,6 @@
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 -
126 126  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  
128 128  We start here with the installation of Brian 2. Brian 2 can be installed simply using the pip command.
... ... @@ -146,17 +146,11 @@
146 146  (% class="box infomessage" %)
147 147  (((
148 148  **Screencast** - terminal
149 -\\(% style="color:#000000" %)python
137 +\\(% 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.
... ... @@ -171,7 +171,7 @@
171 171  \\sudo apt-get install nest
172 172  )))
173 173  
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:
156 +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 Brian 2 on our computer, we can test as follows:
175 175  
176 176  (% class="box infomessage" %)
177 177  (((
... ... @@ -179,52 +179,22 @@
179 179  \\(% style="color:#000000" %)nest
180 180  )))
181 181  
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.
164 +A
183 183  
184 184  (% class="box infomessage" %)
185 185  (((
186 186  **Screencast** - terminal
187 -\\(% style="color:#000000" %)python
169 +\\(% style="color:#000000" %)python3
188 188  \\import nest
189 189  \\exit()
190 190  )))
191 191  
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 -)))
174 +If there are no error messages here, and the import is successful, then we have completed installing NEST simulator.
197 197  
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 on Python.
176 +We next move on to the third simulation, NEURON. The installation for NEURON is a bit more involved.
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:
178 +<< add more >>
201 201  
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 -
227 -
228 228  (% class="box successmessage" %)
229 229  (((
230 230  **Slide** recap of learning objectives