Last modified by spreizer on 2025/08/26 09:19
From version 21.1
edited by spreizer
on 2025/07/30 11:10
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To version 39.1
edited by spreizer
on 2025/08/23 20:11
Change comment: There is no comment for this version

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4 4  (((
5 5  = NEST Tutorials =
6 6  
7 -EBRAINS Swedish Node, Stockholm, 25/08/25 - 27/08/25
7 +EBRAINS Swedish Node Workshop, Stockholm, 26/08/25
8 8  )))
9 9  )))
10 10  
... ... @@ -12,8 +12,10 @@
12 12  (((
13 13  (% class="col-xs-12 col-sm-8" %)
14 14  (((
15 -== From single-cell modeling to large-scale network dynamics with NEST Simulator ==
15 +(% class="wikigeneratedid" id="HFromsingle-cellmodelingtolarge-scalenetworkdynamicswithNESTSimulator" %)
16 +**From single-cell modeling to large-scale network dynamics with NEST Simulator**
16 16  
18 +
17 17  **Instructor**: Sebastian Spreizer, PhD, University of Trier and Research Center Jülich
18 18  
19 19  - [[Tutorial abstract>>url:https://wiki.ebrains.eu/bin/view/Collabs/swedish-node-nest-tutorials/About/]]
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24 24  
25 25  === Time schedule ===
26 26  
27 -|(% style="width:84px" %)9 - 11|(% style="width:235px" %)NEST Desktop|(% style="width:541px" %)[[https:~~/~~/nest-desktop.readthedocs.org/>>https://nest-desktop.readthedocs.org/]]
28 -|(% style="width:84px" %)12 - 15|(% style="width:235px" %)NEST Simulator|(% style="width:541px" %)[[https:~~/~~/nest-simulator.readthedocs.org/>>https://nest-simulator.readthedocs.org/]]
29 -|(% style="width:84px" %)15 - 18|(% style="width:235px" %)NESTML|(% style="width:541px" %)[[https:~~/~~/nestml.readthedocs.org/>>https://nestml.readthedocs.org/]]
29 +|(% style="width:191px" %)10 - 10.30|(% style="width:220px" %)Introduction|(% style="width:422px" %)
30 +|(% style="width:191px" %)10.30 - 12|(% style="width:220px" %)NEST Desktop|(% style="width:422px" %)[[https:~~/~~/nest-desktop.readthedocs.org/>>https://nest-desktop.readthedocs.org/]]
31 +|(% style="width:191px" %)13 - 14.30|(% style="width:220px" %)NEST Simulator|(% style="width:422px" %)[[https:~~/~~/nest-simulator.readthedocs.org/>>https://nest-simulator.readthedocs.org/]]
32 +|(% style="width:191px" %)15 - 16.30|(% style="width:220px" %)NESTML|(% style="width:422px" %)[[https:~~/~~/nestml.readthedocs.org/>>https://nestml.readthedocs.org/]]
30 30  
31 -=== 1) NEST Desktop ===
34 +=== (% style="color:#1a202c; font-family:inherit; font-size:max(23px, min(27px, 15.8889px + 0.925926vw))" %)How to run NEST tutorials on EBRAINS lab?(%%) ===
32 32  
33 -The first part of the tutorial, we look at NEST Desktop.  As a goal we will create and analyze a balanced two-population network.
36 +1. (((
37 +Go to [[https:~~/~~/lab.ebrains.eu>>https://lab.ebrains.eu]]
38 +)))
39 +1. Change drive folder to `/drive/My Libraries/`.
40 +1. (((
41 +Next, clone a repo from the remote Git repository "[[https:~~/~~/gitlab.ebrains.eu/spreizer/nest-tutorials-2025.git>>https://gitlab.ebrains.eu/spreizer/nest-tutorials-2025.git]]" (See red arrow).
34 34  
35 -* [[https:~~/~~/wiki.ebrains.eu/bin/view/Collabs/nest-desktop>>https://wiki.ebrains.eu/bin/view/Collabs/nest-desktop]]
36 36  
37 -=== 2) NEST Simulator ===
44 +[[image:https://wiki.ebrains.eu/bin/download/Collabs/nestml-tutorials/WebHome/1753784762571-499.png?rev=1.1||alt="1753784762571-499.png" data-xwiki-image-style-alignment="center"]]
38 38  
39 -The tutorial will then turn to Jupyter (Python) notebooks where we will start by creating spiking neurons. Here, we learn advanced steps to write code with NEST Simulation syntax. The scripting codes allow us to customize sophisticated use cases with NEST simulations. Examples are:
46 +
47 +)))
48 +1. (((
49 +After cloning, you can find tutorials in respective folders.
40 40  
41 -* neuronal dynamics
42 -* large scale networks,
43 -* networks of spatial neurons
44 -* using plasticity
45 45  
46 -=== 3) NESTML ===
52 +
53 +)))
54 +1. (((
55 +When you start a notebook, select kernel: "EBRAINS-25.02" (or later).
47 47  
48 -The last part is using NESTML to create custom neuron and synapse models for NEST Simulator. A functional plasticity rule will then be introduced into the balanced E/I network to implement a biologically realistic version of reinforcement learning. This will be done by formulating the learning model in the NESTML language syntax, and using the associated toolchain to generate code for NEST [4].
49 49  
50 -* [[https:~~/~~/wiki.ebrains.eu/bin/view/Collabs/nestml-tutorials>>https://wiki.ebrains.eu/bin/view/Collabs/nestml-tutorials]]
58 +[[image:https://wiki.ebrains.eu/bin/download/Collabs/nestml-tutorials/WebHome/1753786904178-861.png?rev=1.1||alt="1753786904178-861.png" data-xwiki-image-style-alignment="center"]]
51 51  
52 52  
53 53  )))
62 +1. Have fun with it!
54 54  
64 +=== Modules ===
55 55  
66 +(% class="wikigeneratedid" %)
67 +**1) NEST Desktop**
68 +
69 +The first part of the tutorial, we look at NEST Desktop.  As a goal we will create and analyze a balanced two-population network.
70 +
71 +[[https:~~/~~/nest-desktop.apps.ebrains.eu/>>https://nest-desktop.apps.ebrains.eu/]]
72 +
73 +More information: [[https:~~/~~/wiki.ebrains.eu/bin/view/Collabs/nest-desktop>>https://wiki.ebrains.eu/bin/view/Collabs/nest-desktop]]
74 +
75 +
76 +(% class="wikigeneratedid" id="H329NESTML" %)
77 +**2) NEST Simulator**
78 +
79 +The tutorial will then turn to Jupyter (Python) notebooks where we will start by creating spiking neurons. Here, we learn advanced steps to write code with NEST Simulation syntax. The scripting codes allow us to customize sophisticated use cases with NEST simulations. How to run examples on EBRAINS lab can be found here:
80 +
81 +More examples: [[https:~~/~~/wiki.ebrains.eu/bin/view/Collabs/nest-simulator-examples/>>https://wiki.ebrains.eu/bin/view/Collabs/nest-simulator-examples/]]
82 +
83 +
84 +**3) NESTML**
85 +
86 +
87 +The last part is using NESTML to create custom neuron and synapse models for NEST Simulator. This will be done by formulating the learning model in the NESTML language syntax, and using the associated toolchain to generate code for NEST Simulator.
88 +
89 +More tutorials: [[https:~~/~~/wiki.ebrains.eu/bin/view/Collabs/nestml-tutorials>>https://wiki.ebrains.eu/bin/view/Collabs/nestml-tutorials]]
90 +)))
91 +
92 +
93 +
94 +[[image:https://www.ebrains.eu/flags/4x3/se.svg||alt="Sweden's flag" data-xwiki-image-style-alignment="center" height="188" width="250"]]
95 +
96 +
56 56  (% class="col-xs-12 col-sm-4" %)
57 57  (((
58 58  {{box title="**Contents**"}}