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  • Ebrains_TVB-NetPyNE_slides.pdf

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2	2
3		-(% class="box" style="text-align: center;" %)
4		-(((
5		-[[**HBP/EBRAINS CodeJam2022**>>https://www.humanbrainproject.eu/en/follow-hbp/events/ebrainshbp-codejam-codejam-12]]
6		-)))
	3	+(% style="text-align: center;" %)
	4	+== **TVB-Multiscale: Deep Brain Stimulation use case demonstration** ==
7	7
8	8	(% style="text-align: center;" %)
9		-=== **TVB-Multiscale: Deep Brain Stimulation TVB-ANNarchy use case demonstration & TVB-NETPYNE demonstration** ===
	7	+== **&** ==
10	10
	9	+(% style="text-align: center;" %)
	10	+== **TVB-NETPYNE demonstration** ==
	11	+
11	11	November 24th, 2022
12	12
13		-== ==
14	14
15		-== (% style="color:#e74c3c" %)**TVB-multiscale JupyterHub apps are now deprecated! See:**(%%) **[[https:~~/~~/wiki.ebrains.eu/bin/view/Collabs/the-virtual-brain-multiscale/>>url:https://wiki.ebrains.eu/bin/view/Collabs/the-virtual-brain-multiscale/]] (% style="color:#e74c3c" %)about how to run TVB-multiscale (TVB-NEST, TVB-NetPyNE (NEURON), TVB-ANNarchy) on EBRAINS!(%%)** ==
16	16
17		-
18	18	=== What can I find here? ===
19	19
20		-* Presentation slides for the [[TVB-Multiscale and for DBS demonstration with TVB-ANNarchy>>attach:2022-11-24_TVB-multiscale_CodeJam2022.pdf]].
21		-* Presentation slides for the [[TVB-NETPYNE demonstration>>attach:Ebrains_TVB-NetPyNE_slides.pdf]].
	18	+* [[Presentation slides>>attach:2022-11-09_TVB-multiscale_SimulateWIthEbrains.pdf]] from the workshop's lecture.
	19	+* The notebook ([[SimulateWithEBRAINS.zip>>path:https://wiki.ebrains.eu/bin/download/Collabs/tvb-multiscale-cosim-mcgillsummerschool/Simulate%20with%20EBRAINS%20TVB-multiscale%20workshop%20presentation/WebHome/SimulateWithEBRAINS.zip?rev=1.1]]) demonstrated during the workshop.
22	22
23	23	=== Guide to run the use-case notebooks ===
24	24
25	25	1. Run the EBRAINS TVB-Multiscale app by browsing to [[https:~~/~~/tvb-multiscale.apps.hbp.eu/>>url:https://tvb-multiscale.apps.hbp.eu/]] and logging in with your EBRAINS account. (The first time you log-in, you might need to try several times by refreshing the page, until it works for you!)
26		-1. Navigate to "TVB-Multiscale-Examples/notebooks" folder, and copy its contents to the "Contributed-Notebooks" folder, which offers user-specific persistent storage.
27		-1. Run the TVB-ANNarchy_DBS_BasalGanglia.ipynb notebook for TVB-ANNarchy DBS Co-Simulation and TVB-NETPYNE_RedWongWang.ipynb for the TVB-NETPYNE Co-Simulation
	24	+1. Navigate to "Contributed-Notebooks" folder, which offers user-specific persistent storage.
	25	+1. Upload and unzip there [[SimulateWithEBRAINS.zip>>path:https://wiki.ebrains.eu/bin/download/Collabs/tvb-multiscale-cosim-mcgillsummerschool/Simulate%20with%20EBRAINS%20TVB-multiscale%20workshop%20presentation/WebHome/SimulateWithEBRAINS.zip?rev=1.1]] by running
	26	+unzip SimulateWithEBRAINS.zip
	27	+on a terminal, or
	28	+! unzip SimulateWithEBRAINS.zip
	29	+in a notebook.
	30	+1. Run the TVB-corr-cortex-opt.ipynb notebook for TVB-ANNarchy cosimulation and the ANNarchy-spiking-cortex.ipynb one for ANNarchy only simulation.

Ebrains_TVB-NetPyNE_slides.pdf

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1		-XWiki.dionperd

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1		-3.1 MB

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