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5		-= TVB for brain states and pathological brain dynamics =
	5	+= Part I-II: TVB for brain states and pathological brain dynamics =
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7	7	Emre Baspinar and Damien Depannemaecker
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15	15	= What can I find here? =
16	16
17		-This collab contains the materials which will be used during the hands-on session on 4 June 2024, during EBRAINS Brain Simulation Workshop taking place in Bilbao: [[https:~~/~~/www.bcamath.org/events/ebrains2024/en/>>https://www.bcamath.org/events/ebrains2024/en/]].
	17	+This collab contains a part of the materials which will be used during the hands-on session on 4 June 2024, during EBRAINS Brain Simulation Workshop taking place in Bilbao: [[https:~~/~~/www.bcamath.org/events/ebrains2024/en/>>url:https://www.bcamath.org/events/ebrains2024/en/]].
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19		-The objective of this hands-on session is to create a familiarity of TVB for the participant by performing simulations related to different brain states. In Part I, we will see a mean-field framework modeling neuronal population dynamics. It is an AdEx mean-field system modeling the population dynamics of a pair of excitatory and inhibitory neuronal populations with adaptation. We will use this framework to simulate brain states at population level. In Part II, we will see that this mean-field framework can be used to approximate the dynamics of a brain region, and a network of these mean-field systems can be used to perform simulations of different brain states on the whole-brain scale via TVB. All these parts can be found in the drive, and they are accessible in the lab.
	19	+The objective of this hands-on session is to create a familiarity of TVB for the participant by performing simulations related to different brain states and epileptic dynamics. At the beginning, we will describe the TVB framework and its building blocks. Then, in Part I, we will see a mean-field framework modeling neuronal population dynamics. We will use this framework to simulate brain states at population level. In Part II, we will see a generalization of this framework to the whole-brain scale via TVB. In Part III, we will see an example epileptic scenario of seizure propagation by using TVB. Part I and Part II can be found in the drive, and they are accessible in the lab. For Part III, we refer to the following collab: [[https:~~/~~/wiki.ebrains.eu/bin/view/Collabs/ebrains-baltic-nordic-school-2024/>>https://wiki.ebrains.eu/bin/view/Collabs/ebrains-baltic-nordic-school-2024/]].
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21	21	= Requirements =
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23	23	Access to the notebooks and materials requires to have an EBRAINS account.
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25		-Participants are also suggested to download the materials in case of connection issues. The material and notebooks can be downloaded by clicking on "Drive" on the left hand side. If the notebooks are locally run, then "%matplotlib widget" should be disabled by commenting it in the corresponding cells.
	25	+Participants are also suggested to download the materials in case of connection issues. The material and notebooks can be downloaded by clicking on "Drive" on the left hand side. Once downloaded, the participants are also suggested to run the cells with the title "Initialization" in "mainAdEx.ipynb" (PART I) and in "Human_TVB_AdEx.ipynb" (PART II) to see and install the necessary packages/dependencies. If the notebooks are run locally, then "%matplotlib widget" should be disabled by commenting it in the relevant cells.
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	27	+TVB installation can be done via the following link: [[https:~~/~~/www.thevirtualbrain.org/tvb/zwei/brainsimulator-software>>url:https://www.thevirtualbrain.org/tvb/zwei/brainsimulator-software]] . Once it is installed, it can be used for a variety of simulations found in EBRAINS Collab.
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28		-Finally, TVB installation can be done via the following link: [[https:~~/~~/www.thevirtualbrain.org/tvb/zwei/brainsimulator-software>>https://www.thevirtualbrain.org/tvb/zwei/brainsimulator-software]]. Once it is installed, it can be used for a variety of simulations which are found on EBRAINS Collab.
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30	30	= References =
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