Attention: The EBRAINS drive will be unavailable for most of the weekend starting the 25th October. Although the Lab is availble while the Drive is down, files that are stored in the Drive will not be loaded and you will be unable to save documents directly on the Lab.


Last modified by ldomide on 2024/04/08 12:55
From version 32.1
edited by dionperd
on 2023/09/26 19:29
Change comment: There is no comment for this version
To version 31.1
edited by dionperd
on 2023/09/26 18:42
Change comment: There is no comment for this version

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20 20  * TVB Dedicated Wiki [[https:~~/~~/wiki.ebrains.eu/bin/view/Collabs/the-virtual-brain/>>url:https://wiki.ebrains.eu/bin/view/Collabs/the-virtual-brain/]]
21 21  * TVB in HBP User Story [[https:~~/~~/wiki.ebrains.eu/bin/view/Collabs/user-story-tvb/>>url:https://wiki.ebrains.eu/bin/view/Collabs/user-story-tvb/]]
22 22  
23 +(% class="wikigeneratedid" %)
23 23  == ==
24 24  
26 +(% class="wikigeneratedid" %)
25 25  == Running TVB-MULTISCALE at EBRAINS JupyterLab ==
26 26  
27 -TVB-multiscale is made available at [[EBRAINS JupyterLab>>https://lab.ebrains.eu/]].
29 +TVB-multiscale is made available at [[EBRAINS JupyterLab>>https://lab.ebrains.eu/]]. All the user has to do is login with the EBRAINS credentials, and start a Python console or a Jupyter notebook, TVB-multiscale being available for importing (e.g., via "import tvb_multiscale"). All necessary TVB-multiscale dependencies (NEST, ANNarchy, NetPyNE (NEURON), Elephant, Pyspike) are also installed and available. We suggest the users to upload [[documented notebooks>>https://github.com/the-virtual-brain/tvb-multiscale/tree/master/docs/notebooks]] and/or [[examples' scripts and notebooks >>https://github.com/the-virtual-brain/tvb-multiscale/tree/master/examples]]from TVB-multiscale Github repository and run them there.
28 28  
29 -All the user has to do is login with the EBRAINS credentials, and start a Python console or a Jupyter notebook, TVB-multiscale being available for importing (e.g., via "import tvb_multiscale").
30 30  
31 -All necessary TVB-multiscale dependencies (NEST, ANNarchy, NetPyNE (NEURON), Elephant, Pyspike) are also installed and available.
32 -
33 -We suggest the users to upload [[documented notebooks>>https://github.com/the-virtual-brain/tvb-multiscale/tree/master/docs/notebooks]] and/or [[examples' scripts and notebooks >>https://github.com/the-virtual-brain/tvb-multiscale/tree/master/examples]]from TVB-multiscale Github repository and run them there.
34 -
35 -Alternatively, users can sparse checkout the docs and examples folders of TVB-multiscale Github repo, via the following sequence of commands in a terminal or in Jupyter notebook's cells (for notebooks you need to use "!" before each command!):
36 -
37 -~1. Get into the user's My Libraries folder:
38 -
39 -{{{cd /mnt/user/drive/My Libraries}}}
40 -
41 -2. Create a folder, e.g., "tvb-multiscale-examples"
42 -
43 -{{{mkdir tvb-multiscale-examples}}}
44 -
45 -3. Create an empty git repository:
46 -
47 -{{{git init
48 -
49 -3. Add tvb-multiscale remote:
50 -git remote add -f origin }}}
51 -
52 -This fetches all objects but doesn't check them out.
53 -
54 -4. Allow for sparse checkout in git config:
55 -
56 -{{{git config core.sparseCheckout true
57 -}}}
58 -
59 -5. Add the docs and examples folders to the ones to be checked out:
60 -
61 -{{{echo "docs" >> .git/info/sparse-checkout
62 -
63 -echo "examples" >> .git/info/sparse-checkout}}}
64 -
65 -6. Finally, pull the master from the remote:
66 -
67 -{{{git pull origin master}}}
68 -
69 -which will download the specified folders.
70 -
71 -All these steps can of course be made from any user fork of the TVB-multiscale repository.
72 -
73 -Last but not least, users will also have to modify the attribute config.DEFAULT_CONNECTIVITY_ZIP of the base configuration class Config in all cases of examples and notebooks, to be able to load a default TVB connectivity for the simulations to run.  For instance, in the above example, the correct path would be:
74 -
75 -{{{config.DEFAULT_CONNECTIVITY_ZIP = "/mnt/user/drive/My Libraries/tvb-multiscale-examples/examples/data/tvb_data/berlinSubjects/QL_20120814/QL_20120814_Connectivity.zip" }}}
76 -
77 -
78 78  == Use our Jupyter Hub setup online ((% style="color:#c0392b" %)DEPRECATED(%%)) ==
79 79  
80 80  (% style="color:#c0392b" %)**TVB-multiscale app is deprecated and will stop being available after the end of 2023!**
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102 102  
103 103  This is the path recommended for people working closely with tvb-multiscale. They are able to download it in their local work env and code freely and fast with it.
104 104  
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105 105  == ==
106 106  
107 107  == Running TVB-MULTISCALE jobs on CSCS infrastructure from HBP collab ==