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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/]]
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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 case of the above folder structure after sparse checkout, and assuming that the user runs 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		-
79	79	== Use our Jupyter Hub setup online ((% style="color:#c0392b" %)DEPRECATED(%%)) ==
80	80
81	81	(% style="color:#c0392b" %)**TVB-multiscale app is deprecated and will stop being available after the end of 2023!**
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103	103
104	104	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.
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106	106	== ==
107	107
108	108	== Running TVB-MULTISCALE jobs on CSCS infrastructure from HBP collab ==