Version 24.1 by michaels on 2021/04/16 21:32
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5 = TVB C ~-~- High-speed parallel brain network models =
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7 A fast implementation of The Virtual Brain brain network simulator
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9 [[Direct link to notebook>>https://drive.ebrains.eu/#my-libs/lib/f5e40b3b-91cb-4671-9178-4d2673ad8ac4]]
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11 [[image:4144.jpeg]]
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19 == Quick links ==
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21 * [[TVB on EBRAINS (Short Version)>>https://www.youtube.com/watch?v=_G_DjRb1ams&feature=youtu.be||rel="noopener noreferrer" target="_blank"]]
22 * [[TVB on EBRAINS (Long Version)>>https://www.youtube.com/watch?v=eZrh6ztGFAY&feature=youtu.be||rel="noopener noreferrer" target="_blank"]]
23 * [[TVB on EBRAINS (Mini Videos)>>https://www.youtube.com/playlist?list=PLVtblERyzDeLcVv4BbW3BvmO8D-qVZxKf||rel="noopener noreferrer" target="_blank"]]
24 * [[User Story>>https://wiki.ebrains.eu/bin/view/Collabs/user-story-tvb/||rel="noopener noreferrer" target="_blank"]]
25
26 == What can I find here? ==
27
28 * an IPython notebook that describes how to
29 ** pull the TVB-C container into one of the associated supercomputers using PyUnicore
30 ** upload model data to the supercomputer
31 ** set up and run simulations
32 ** download simulation results
33
34 == How do I use it? ==
35
36 * the simulation code is implemented as a Docker container
37 * the container is executed on supercomputers and operated via IPython notebooks
38 * Find the notebook by clicking on "Drive" in the left menu. The notebook is called "TVB_C.ipynb"
39 * To use the notebook, download it onto your local filesystem, create a new Collab and upload it there.
40 * Then, head over to [[https:~~/~~/lab.ebrains.eu/>>url:https://lab.ebrains.eu/]] to edit and run your notebook.
41 * Depending on whether you created a public or a private notebook it will be accessible in either "drive/Shared with all" or "drive/Shared with groups'"
42
43 == Metadata ==
44
45 |=(((
46 |=Category|tool
47 |=Tags|(((
48 * [[brain-network-model>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
49 * [[TVB>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
50 * [[high-performance>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
51 * [[parallel>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
52 * [[HPC>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
53 * [[supercomputer>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
54 * [[brain-simulation>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
55 * [[connectome>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
56 * [[functional-connectivity>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
57 * [[The-Virtual-Brain>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
58 )))
59 |=Partners|(((
60 * Charité Universitätsmedizin Berlin [[CHARITE>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
61 )))
62 |=Maintainers|(((
63 * [[Petra Ritter>>path:mailto:petra.ritter@charite.de]]
64 * [[Michael Schirner>>path:mailto:michael.schirner@charite.de]]
65 )))
66 |=Homepage|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/fast_tvb>>url:https://hub.docker.com/r/thevirtualbrain/fast_tvb]]
67 |=Documentation|[[https:~~/~~/collab.humanbrainproject.eu/#/collab/65304/nav/444404>>url:https://collab.humanbrainproject.eu/#/collab/65304/nav/444404]]
68 |=Support|[[michael.schirner@charite.de>>path:mailto:michael.schirner@charite.de]]
69 |=Source Code|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/fast_tvb>>url:https://hub.docker.com/r/thevirtualbrain/fast_tvb]]
70 |=Download Page|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/fast_tvb>>url:https://hub.docker.com/r/thevirtualbrain/fast_tvb]]
71 |=License|GPL3
72 |=Current Version|1.0
73 |=All Versions|(((
74 * 1.0
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77
78 == Publications using TVB C ==
79
80 * [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/29308767>>url:https://www.ncbi.nlm.nih.gov/pubmed/29308767]]
81 * [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/32194282>>url:https://www.ncbi.nlm.nih.gov/pubmed/32194282]]
82 * [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/29911173>>url:https://www.ncbi.nlm.nih.gov/pubmed/29911173]]
83 * [[https:~~/~~/www.thieme-connect.com/products/ejournals/html/10.1055/s-0039-3403020>>url:https://www.thieme-connect.com/products/ejournals/html/10.1055/s-0039-3403020]]
84 * [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/?term=31316116>>url:https://www.ncbi.nlm.nih.gov/pubmed/?term=31316116]]
85 * [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/?term=30035018>>url:https://www.ncbi.nlm.nih.gov/pubmed/?term=30035018]]
86 * [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/?term=27041212>>url:https://www.ncbi.nlm.nih.gov/pubmed/?term=27041212]]
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92 {{box title="**Contents**"}}
93 {{toc/}}
94 {{/box}}
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