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Last modified by ldomide on 2024/04/08 12:55
From version 36.2
edited by vbragin
on 2024/03/02 12:30
Change comment: There is no comment for this version
To version 34.1
edited by dionperd
on 2023/09/26 19:34
Change comment: There is no comment for this version

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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 log in with their EBRAINS credentials, and start a Python console or a Jupyter notebook using the kernel "EBRAINS-23.09" (or a more recent version), where TVB-multiscale can be imported (e.g., via "import tvb_multiscale"). All necessary TVB-multiscale dependencies (NEST, ANNarchy, NetPyNE (NEURON), Elephant, Pyspike) are also installed and available.
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 -This collab contains various examples of using TVB-Multiscale with all three supported spiking simulators. We suggest copying the contents of this collab to your Library or to any collab owned by you, and running them there (note that the user's drive offers persistent storage, i.e. users will find their files after logging out and in again), as follows:
31 +All necessary TVB-multiscale dependencies (NEST, ANNarchy, NetPyNE (NEURON), Elephant, Pyspike) are also installed and available.
32 32  
33 -~1. Select `Drive` on the left of the current page (or use [[this link>>https://wiki.ebrains.eu/bin/view/Collabs/the-virtual-brain-multiscale/Drive]]).
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 34  
35 -2. Check the `tvb-multiscale-collab` folder checkbox, and copy it to your `My Library` ("copy" icon will appear above the files/folders list).
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  
37 -3. Select `Lab` (on the left), and navigate to the destination where you just copied the folder.
37 +~1. Get into the user's My Libraries folder:
38 38  
39 -4. Enter the `tvb-multiscale-collab` folder, and open either of example notebooks. Ensure you select the appropriate ipykernel (EBRAINS-23.09 or a more recent one)
39 +{{{cd /mnt/user/drive/My Libraries}}}
40 40  
41 +2. Create a folder, e.g., "tvb-multiscale-examples"
41 41  
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 initiated 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 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 +
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 +
42 42  == Use our Jupyter Hub setup online ((% style="color:#c0392b" %)DEPRECATED(%%)) ==
43 43  
44 44  (% style="color:#c0392b" %)**TVB-multiscale app is deprecated and will stop being available after the end of 2023!**