Wiki source code of EBRAINS Bilbao TVB Hands-on

Version 16.1 by emrebasp on 2024/05/30 11:00

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7.1	5	= TVB for brain states and pathological brain dynamics =
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7.1	7	Emre Baspinar and Damien Depannemaecker
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	15	= What can I find here? =
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10.1	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/]].
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16.1	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.
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7.1	21	= Requirements =
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10.1	23	Access to the notebooks and materials requires to have an EBRAINS account.
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16.1	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.
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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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10.2	30	= References =
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	33	* Baspinar, E., Cecchini, G., DePass, M., Andujar, M., Pani, P., Ferraina, S., Moreno-Bote, R., Cos, I., Destexhe, A. (2023). [[A biologically plausible decision-making model based on interacting cortical columns>>https://www.biorxiv.org/content/10.1101/2023.02.28.530384v2]]. bioRxiv, 2023-02.
	34	* Di Volo, M., Romagnoni, A., Capone, C., Destexhe, A. (2019). [[Biologically realistic mean-field models of conductance-based networks of spiking neurons with adaptation>>https://direct.mit.edu/neco/article-abstract/31/4/653/8461/Biologically-Realistic-Mean-Field-Models-of?redirectedFrom=fulltext]]. Neural Computation, 31(4), 653-680.
	35	* Goldman, J. S., Kusch, L., Aquilue, D., Yalçınkaya, B. H., Depannemaecker, D., Ancourt, K., Nghiem, T. E., Jirsa, V., Destexhe, A. (2023). [[A comprehensive neural simulation of slow-wave sleep and highly responsive wakefulness dynamics>>https://www.frontiersin.org/articles/10.3389/fncom.2022.1058957/full]]. Frontiers in Computational Neuroscience, 16, 1058957.
	36	* Sacha, M., Goldman, J. S., Kusch, L., Destexhe, A. (2024). [[Asynchronous and slow-wave oscillatory states in connectome-based models of mouse, monkey and human cerebral cortex>>https://www.mdpi.com/2076-3417/14/3/1063]]. Applied Sciences, 14(3), 1063.
	37	* Sanz-Leon P., Knock S. A., Spiegler A., Jirsa V. K. (2015). [[Mathematical framework for large-scale brain network modeling in The Virtual Brain>>url:https://www.sciencedirect.com/science/article/pii/S1053811915000051]]. NeuroImage, 111, 385-430.
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	48	{{box title="Contents"}}
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