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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" %)
24	24	== ==
25	25
26		-(% class="wikigeneratedid" %)
27	27	== Running TVB-MULTISCALE at EBRAINS JupyterLab ==
28	28
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.
	27	+TVB-multiscale is made available at [[EBRAINS JupyterLab>>https://lab.ebrains.eu/]].
30	30
	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").
31	31
	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 (please note that the user's drive offers persistent storage, i.e., users will find their files after logging out and in again).
	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-collab"
	42	+
	43	+{{{mkdir tvb-multiscale-collab}}}
	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	+
32	32	== Use our Jupyter Hub setup online ((% style="color:#c0392b" %)DEPRECATED(%%)) ==
33	33
34	34	(% style="color:#c0392b" %)**TVB-multiscale app is deprecated and will stop being available after the end of 2023!**
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56	56
57	57	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.
58	58
59		-(% class="wikigeneratedid" %)
60	60	== ==
61	61
62	62	== Running TVB-MULTISCALE jobs on CSCS infrastructure from HBP collab ==