Last modified by adavison on 2022/10/04 13:53
From version 50.1
edited by shailesh
on 2021/12/09 17:19
Change comment: There is no comment for this version
To version 44.1
edited by annedevismes
on 2021/10/19 09:43
Change comment: There is no comment for this version

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Author
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1 -XWiki.shailesh
1 +XWiki.annedevismes
Content
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37 37  **Slide** listing learning objectives
38 38  )))
39 39  
40 -In this tutorial, I will guide you through setting up PyNN, together with the Brian 2, NEST, and NEURON 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.
40 +In this tutorial, I will guide you through setting up PyNN, together with the Brian 2, NEST, and NEURON, and 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.
41 41  
42 42  (% class="box successmessage" %)
43 43  (((
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123 123  You might be required to run the above command every time you open a new terminal window. Check 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 -Before we proceed, let us run the following commands to ensure that our environment is setup as required:
127 -
128 -
129 -(% class="box infomessage" %)
130 -(((
131 -**Screencast** - terminal
132 -\\(% style="color:#000000" %)pip install ~-~-upgrade pip
133 -sudo apt install make
134 -)))
135 -
136 136  Now that we have our project's virtual environment setup, we are 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 will demonstrate the installation of Brian2, NEST, and NEURON simulators.
137 137  
138 138  (% class="box errormessage" %)
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194 194  (((
195 195  **Screencast** - terminal
196 196  \\(% style="color:#000000" %)nest
197 -
198 -(% style="color:#000000" %)exit
199 199  )))
200 200  
201 201  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. Next, let's verify that this is indeed accessible via Python.
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297 297  
298 298  This confirms that all the required software packages have been successfully completed and are functioning as expected.
299 299  
300 -As a last step, we will install a Python package named 'matplotlib' that would come in handy in the tutorials ahead.
301 -
302 -(% class="box infomessage" %)
303 -(((
304 -**Screencast** - terminal
305 -\\(% style="color:#000000" %)pip install matplotlib
306 -)))
307 -
308 308  (% class="box successmessage" %)
309 309  (((
310 310  **Slide** recap of learning objectives