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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 35.1
edited by dionperd
on 2023/09/26 19:39
Change comment: There is no comment for this version

Summary

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... ... @@ -26,11 +26,11 @@
26 26  
27 27  TVB-multiscale is made available at [[EBRAINS JupyterLab>>https://lab.ebrains.eu/]].
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").
29 +All the user has to do is login with their 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 31  All necessary TVB-multiscale dependencies (NEST, ANNarchy, NetPyNE (NEURON), Elephant, Pyspike) are also installed and available.
32 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.
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 (please note that the user's drive offers persistent storage, i.e., users will find their files after logging out and in again).
34 34  
35 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 36  
... ... @@ -68,13 +68,14 @@
68 68  
69 69  which will download the specified folders.
70 70  
71 -All these steps can of course be made from any user fork of the TVB-multiscale repository.
71 +All these steps can of course be made from any user initiated fork of the TVB-multiscale repository.
72 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:
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 case of the above folder structure after sparse checkout, and for the example of the [[documented TVB-NEST_WilsonCowan.ipynb notebook>>https://github.com/the-virtual-brain/tvb-multiscale/blob/master/docs/notebooks/TVB-NEST_WilsonCowan.ipynb]], the correct path would be:
74 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" }}}
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 76  
77 77  
78 +
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!**