Changes for page User Story: TVB

Last modified by ldomide on 2024/05/20 08:51

From version 48.1
edited by ldomide
on 2022/04/18 15:09
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To version 50.1
edited by ldomide
on 2024/05/20 08:51
Change comment: There is no comment for this version

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67 67  TVB can be operated via GUI and programmatic Python interface.
68 68  
69 69  * On the EBRAINS Collaboratory Platform TVB Simulator usage is introduced through IPython Notebooks in the main TVB [[collab>>doc:Collabs.the-virtual-brain.WebHome||target="_blank"]].
70 -* Additionally, the TVB GUI can be directly accessed as [[a Web App>>https://tvb.apps.hbp.eu/]]. Via the Web App users can configure simulations that are – depending on their complexity – either simulated directly on the web server or on a supercomputer, thereby making resource-consuming TVB functionality accessible to researchers that do not have access to supercomputers.
71 -* Compiled standalone versions of the main software package can be downloaded from [[thevirtualbrain.org>>www.thevirtualbrain.org]].
70 +* Additionally, the TVB GUI can be directly accessed as [[a Web App>>https://tvb.apps.ebrains.eu/]]. Via the Web App users can configure simulations that are – depending on their complexity – either simulated directly on the web server or on a supercomputer, thereby making resource-consuming TVB functionality accessible to researchers that do not have access to supercomputers.
71 +* Compiled standalone versions of the main software package can be downloaded from [[thevirtualbrain.org>>http://www.thevirtualbrain.org]].
72 72  
73 -
74 74  In the following we take you through the main steps of brain network model simulation:
75 75  
76 76  * Construct and downloaded the structural connectivity generated with the TVB pipeline. Alternatively, you can use demo SC that is shipped with the main TVB package.
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85 85  
86 86  == TVB+NEST: Multiscale simulation ==
87 87  
88 -In the previous step we simulated the brain at a coarse spatial resolution: the macroscopic scale of brain regions (e.g. “M1”, “V1”, etc.) and long-range white matter fiber bundles. However, interesting computations often happen on smaller scales, like the mesoscopic scale of small neural populations or the microscopic scale of individual neurons and neural networks. TVB+NEST is a Python toolbox that makes it easier to simulate multi-scale networks, i.e., networks, where one part simulates activity on a coarse scale and another part simulates activity on a finer scale. Essentially, TVB+NEST is a Python wrapper for The Virtual Brain neuroinformatics platform and the NEST spiking network simulator. TVB+NEST exists as a web app and a download version. The web app runs on HBP computers, while the download version is implemented as standalone Docker container that can be downloaded. To run TVB+NEST follow the code [[here>>https://github.com/the-virtual-brain/tvb-multiscale]] or directly open the App [[here>>https://tvb-nest.apps.hbp.eu/hub/login]].
87 +In the previous step we simulated the brain at a coarse spatial resolution: the macroscopic scale of brain regions (e.g. “M1”, “V1”, etc.) and long-range white matter fiber bundles. However, interesting computations often happen on smaller scales, like the mesoscopic scale of small neural populations or the microscopic scale of individual neurons and neural networks. TVB+NEST is a Python toolbox that makes it easier to simulate multi-scale networks, i.e., networks, where one part simulates activity on a coarse scale and another part simulates activity on a finer scale. Essentially, TVB+NEST is a Python wrapper for The Virtual Brain neuroinformatics platform and the NEST spiking network simulator. TVB+NEST exists as a web app and a download version. The web app runs on HBP computers, while the download version is implemented as standalone Docker container that can be downloaded. To run TVB+NEST follow the code [[here>>https://github.com/the-virtual-brain/tvb-multiscale]] or directly use the python module in [[EBRAINS Lab>>https://lab.ebrains.eu/]] (where it was installed as a Spack package).
89 89  
90 90  Alternatively, download the standalone Docker container thevirtualbrain/tvb-nest from Dockerhub. In the previous sections you may have simulated a large-scale brain model, but are now interested how large-scale activity affects finer-scale activity in a specific region. To familiarize yourself with TVB+NEST, you may read more [[here>>https://wiki.ebrains.eu/bin/view/Collabs/the-virtual-brain-multiscale/]].
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