Last modified by spreizer on 2025/08/26 09:19
From version 42.1
edited by spreizer
on 2025/08/23 20:18
Change comment: There is no comment for this version
To version 37.2
edited by spreizer
on 2025/08/23 20:01
Change comment: There is no comment for this version

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12 12  (((
13 13  (% class="col-xs-12 col-sm-8" %)
14 14  (((
15 -(% class="wikigeneratedid" id="HFromsingle-cellmodelingtolarge-scalenetworkdynamicswithNESTSimulator" %)
16 -**From single-cell modeling to large-scale network dynamics with NEST Simulator**
15 +== From single-cell modeling to large-scale network dynamics with NEST Simulator ==
17 17  
18 18  
19 19  **Instructor**: Sebastian Spreizer, PhD, University of Trier and Research Center Jülich
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21 21  - [[Tutorial abstract>>url:https://wiki.ebrains.eu/bin/view/Collabs/swedish-node-nest-tutorials/About/]]
22 22  
23 23  
24 -The tutorial is composed of three modules in which the user learns to simulate with NEST step by step.
23 +The tutorial is composed of three parts in which the user learns to simulate with NEST step by step.
25 25  
26 26  
27 27  === Time schedule ===
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31 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 32  |(% style="width:191px" %)15 - 16.30|(% style="width:220px" %)NESTML|(% style="width:422px" %)[[https:~~/~~/nestml.readthedocs.org/>>https://nestml.readthedocs.org/]]
33 33  
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?(%%) ===
33 +=== 1) NEST Desktop ===
35 35  
36 -1. (((
37 -Go to [[https:~~/~~/lab.jsc.ebrains.eu>>https://lab.jsc.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]]" (Click on [[image:1755972938026-462.png||height="30" width="28"]]).
35 +The first part of the tutorial, we look at NEST Desktop.  As a goal we will create and analyze a balanced two-population network.
42 42  
37 +* [[https:~~/~~/nest-desktop.apps.ebrains.eu/>>https://nest-desktop.apps.ebrains.eu/]]
38 +* [[https:~~/~~/wiki.ebrains.eu/bin/view/Collabs/nest-desktop>>https://wiki.ebrains.eu/bin/view/Collabs/nest-desktop]]
43 43  
44 -[[image:1755972871032-845.png||data-xwiki-image-style-alignment="center"]]
40 +=== 2) NEST Simulator ===
45 45  
46 -
47 -)))
48 -1. (((
49 -After cloning, you find tutorials in `nest-tutorials-2025` folders.
42 +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:
50 50  
51 -
52 -)))
53 -1. (((
54 -When you start a notebook, select kernel: "EBRAINS-25.02" (or later).
44 +* [[https:~~/~~/wiki.ebrains.eu/bin/view/Collabs/nest-simulator-examples/>>https://wiki.ebrains.eu/bin/view/Collabs/nest-simulator-examples/]]
55 55  
46 +=== 3) NESTML ===
56 56  
57 -[[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"]]
48 +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.
58 58  
59 -
60 -)))
61 -1. Have fun with it!
50 +* [[https:~~/~~/wiki.ebrains.eu/bin/view/Collabs/nestml-tutorials>>https://wiki.ebrains.eu/bin/view/Collabs/nestml-tutorials]]
62 62  
63 -=== Modules ===
64 64  
53 +== How to run NEST tutorials on EBRAINS lab? ==
65 65  
66 -(% class="wikigeneratedid" %)
67 -**1) NEST Desktop**
55 +1. Go to [[https:~~/~~/lab.ebrains.eu>>https://lab.ebrains.eu]](((
56 +
57 +)))
58 +1. (((
59 +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).
68 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 70  
71 -[[https:~~/~~/nest-desktop.apps.ebrains.eu/>>https://nest-desktop.apps.ebrains.eu/]]
62 +[[image:1753784762571-499.png||data-xwiki-image-style-alignment="center"]]
72 72  
73 -More information: [[https:~~/~~/wiki.ebrains.eu/bin/view/Collabs/nest-desktop>>https://wiki.ebrains.eu/bin/view/Collabs/nest-desktop]]
74 74  
65 +{{info}}
66 +If you want to have it persistently, cloned it into your drive folder "/drive/My Libraries/".
67 +{{/info}}
75 75  
76 -(% class="wikigeneratedid" id="H329NESTML" %)
77 -**2) NEST Simulator**
69 +
70 +)))
71 +1. (((
72 +After cloning, you can find tutorials in respective folders.
78 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 80  
81 -More examples: [[https:~~/~~/wiki.ebrains.eu/bin/view/Collabs/nest-simulator-examples/>>https://wiki.ebrains.eu/bin/view/Collabs/nest-simulator-examples/]]
75 +[[image:1753784886260-197.png||data-xwiki-image-style-alignment="center"]]
82 82  
77 +
78 +)))
79 +1. (((
80 +When you start a notebook, select kernel: "EBRAINS-25.02" (or later).
83 83  
84 -**3) NESTML**
85 85  
83 +[[image:1753786904178-861.png||data-xwiki-image-style-alignment="center"]]
86 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]]
85 +
90 90  )))
87 +1. Have fun with it!
88 +)))
91 91  
92 92  
93 93  
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