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  • BasalGanglia.ipynb

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2	2	//McGill University "Summer School in Nonlinear Dynamics for the Life Sciences with Applications to Neuroscience and Psychology" (June 2021)//
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4		-== What can I find here? ==
	4	+(% class="wikigeneratedid" id="HTVB-multiscaleJupyterHubappsarenowdeprecated21See:A0https:2F2Fwiki.ebrains.eu2Fbin2Fview2FCollabs2Fthe-virtual-brain-multiscale2FA0abouthowtorunTVB-multiscale28TVB-NEST2CTVB-NetPyNE28NEURON292CTVB-ANNarchy29onEBRAINS21" %)
	5	+(% 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!(%%)**
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	7	+
	8	+=== ===
	9	+
	10	+=== What can I find here? ===
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6	6	* Presentation slides from the Summer School lecture on TVB-multiscale cosimulation ([[2021-06-07-McGill_VirtualCourse.pdf>>https://drive.ebrains.eu/lib/14db5dbf-97c8-4971-86e5-9b15fd57dd87/file/MacGillSummerSchool/2021-06-07-McGill_VirtualCourse.pdf]]).
7	7	* [[Homework materials>>https://drive.ebrains.eu/#my-libs/lib/14db5dbf-97c8-4971-86e5-9b15fd57dd87/MacGillSummerSchool/Homework]] including a use case of a TVB - Spiking Basal Ganglia multiscale cosimulation notebook (see also attached .zip file at the current page)
8	8	* [[Homework solutions>>https://drive.ebrains.eu/lib/14db5dbf-97c8-4971-86e5-9b15fd57dd87/file/MacGillSummerSchool/HomeworkSolutions.zip]] and [[Homework solutions' outputs>>https://drive.ebrains.eu/lib/14db5dbf-97c8-4971-86e5-9b15fd57dd87/file/MacGillSummerSchool/HomeworkSolutionsOutputs.zip]] (see also attached .zip files at the current page; password protected)
	15	+* The notebook [[BasalGanglia.ipynb>>https://wiki.ebrains.eu/bin/download/Collabs/tvb-multiscale-cosim-mcgillsummerschool/5thTVBinEBRAINSworkshop20210604/WebHome/BasalGanglia.ipynb?rev=1.1]] used for the demonstration of this TVB-multiscale use case during the lecture.
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10	10	=== Guide to run the use-case notebook ===
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12		-1. Run the TVB-NEST app by browsing to [[https:~~/~~/tvb-multiscale.apps.hbp.eu/>>https://tvb-multiscale.apps.hbp.eu/]] and logging in with your EBRAINS account.
	19	+1. Run the TVB-Multiscale app by browsing to [[https:~~/~~/tvb-multiscale.apps.hbp.eu/>>https://tvb-multiscale.apps.hbp.eu/]] and logging in with your EBRAINS account.
13	13	1. Navigate to "ContributedNotebooks" folder, which offers persistent storage for EBRAINS users.
14	14	1. You will need the notebook [[BasalGangliaHomework.ipynb>>https://drive.ebrains.eu/lib/14db5dbf-97c8-4971-86e5-9b15fd57dd87/file/MacGillSummerSchool/Homework/BasalGangliaHomework.ipynb]], the data folder [[basal_ganglia_conn>>https://drive.ebrains.eu/#my-libs/lib/14db5dbf-97c8-4971-86e5-9b15fd57dd87/MacGillSummerSchool/Homework/basal_ganglia_conn]], and the pictures folder [[pics>>https://drive.ebrains.eu/#my-libs/lib/14db5dbf-97c8-4971-86e5-9b15fd57dd87/MacGillSummerSchool/Homework/pics]], found in the [[drive folder Homework/McGillSummerSchool>>https://drive.ebrains.eu/#my-libs/lib/14db5dbf-97c8-4971-86e5-9b15fd57dd87/MacGillSummerSchool/Homework]]. All materials can also be found as the file [[Homework.zip>>https://wiki.ebrains.eu/bin/download/Collabs/tvb-multiscale-cosim-mcgillsummerschool/5thTVBinEBRAINSworkshop20210604/WebHome/Homework.zip?rev=1.1]] attached to the current page (scroll down to find it).
15	15	1. The easiest way to get the above materials is to upload Homework.zip to "ContributedNotebooks" folder, and run the command
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16	16	! unzip ./Homework.zip
17	17	on a cell of a new notebook, from within the same folder.
18	18	1. Finally, navigate inside the decompressed Homework folder and run the notebook BasalGangliaHomework.ipynb. Your results will be saved in your personal drive space and can be found in the "ContributedNotebooks" folder whenever you log in again to the app.
	26	+1. You can also run the lecture notebook [[BasalGanglia.ipynb>>https://wiki.ebrains.eu/bin/download/Collabs/tvb-multiscale-cosim-mcgillsummerschool/5thTVBinEBRAINSworkshop20210604/WebHome/BasalGanglia.ipynb?rev=1.1]] in a similar manner, if you upload it to the same path where [[basal_ganglia_conn>>https://drive.ebrains.eu/#my-libs/lib/14db5dbf-97c8-4971-86e5-9b15fd57dd87/MacGillSummerSchool/Homework/basal_ganglia_conn]], and the pictures folder [[pics>>https://drive.ebrains.eu/#my-libs/lib/14db5dbf-97c8-4971-86e5-9b15fd57dd87/MacGillSummerSchool/Homework/pics]] are.
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BasalGanglia.ipynb

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