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5 -= TVB for brain states and pathological brain dynamics =
5 += My Collab's Extended Title =
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7 -Emre Baspinar and Damien Depannemaecker
7 +My collab's subtitle
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15 15  = What can I find here? =
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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 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/]].
21 += Who has access? =
20 20  
21 -= Requirements =
22 -
23 -Access to the notebooks and materials requires to have an EBRAINS account.
24 -
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. The participants are also suggested to run the cells with the title "Initialization" in If the notebooks are run locally, then "%matplotlib widget" should be disabled by commenting it in the corresponding cells.
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28 -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.
29 -
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.
23 +Describe the audience of this collab.
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