Version 20.1 by michaels on 2020/07/06 09:36
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michaels 7.1 5 = TVB C ~-~- High-speed parallel brain network models =
michaels 1.1 6
michaels 7.1 7 A fast implementation of The Virtual Brain brain network simulator
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michaels 17.1 9 [[Direct link to notebook>>https://drive.ebrains.eu/#my-libs/lib/f5e40b3b-91cb-4671-9178-4d2673ad8ac4]]
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michaels 12.1 11 [[image:4144.jpeg]]
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20 == Quick links ==
21
22 * [[TVB on EBRAINS (Short Version)>>https://www.youtube.com/watch?v=_G_DjRb1ams&feature=youtu.be||rel=" noopener noreferrer" target="_blank"]]
23 * [[TVB on EBRAINS (Long Version)>>https://www.youtube.com/watch?v=eZrh6ztGFAY&feature=youtu.be||rel=" noopener noreferrer" target="_blank"]]
24 * [[TVB on EBRAINS Mini Videos>>https://www.youtube.com/playlist?list=PLVtblERyzDeLcVv4BbW3BvmO8D-qVZxKf||rel=" noopener noreferrer" target="_blank"]]
25 * [[User Story>>https://wiki.ebrains.eu/bin/view/Collabs/user-story-tvb/||rel=" noopener noreferrer" target="_blank"]]
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michaels 13.1 27 == What can I find here? ==
michaels 1.1 28
michaels 7.1 29 * an IPython notebook that describes how to
30 ** pull the TVB-C container into one of the associated supercomputers using PyUnicore
31 ** upload model data to the supercomputer
32 ** set up and run simulations
33 ** download simulation results
michaels 8.1 34
35 == How do I use it? ==
36
37 * the simulation code is implemented as a Docker container
38 * the container is executed on supercomputers and operated via IPython notebooks
39 * Find the notebook by clicking on "Drive" in the left menu. The notebook is called "TVB_C.ipynb"
40 * To use the notebook, download it onto your local filesystem, create a new Collab and upload it there.
41 * Then, head over to [[https:~~/~~/lab.ebrains.eu/>>url:https://lab.ebrains.eu/]] to edit and run your notebook.
42 * 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'"
michaels 13.1 43
michaels 14.1 44 == Metadata ==
michaels 13.1 45
michaels 19.1 46 |=(((
47 |=Category|tool
48 |=Tags|(((
49 * [[brain-network-model>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
50 * [[TVB>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
51 * [[high-performance>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
52 * [[parallel>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
53 * [[HPC>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
54 * [[supercomputer>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
55 * [[brain-simulation>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
56 * [[connectome>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
57 * [[functional-connectivity>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
58 * [[The-Virtual-Brain>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
59 )))
michaels 18.1 60 |=Partners|(((
61 * Charité Universitätsmedizin Berlin [[CHARITE>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
62 )))
63 |=Maintainers|(((
64 * [[Petra Ritter>>path:mailto:petra.ritter@charite.de]]
michaels 19.1 65 * [[Michael Schirner>>path:mailto:michael.schirner@charite.de]]
michaels 18.1 66 )))
michaels 19.1 67 |=Homepage|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/fast_tvb>>url:https://hub.docker.com/r/thevirtualbrain/fast_tvb]]
68 |=Documentation|[[https:~~/~~/collab.humanbrainproject.eu/#/collab/65304/nav/444404>>url:https://collab.humanbrainproject.eu/#/collab/65304/nav/444404]]
69 |=Support|[[michael.schirner@charite.de>>path:mailto:michael.schirner@charite.de]]
70 |=Source Code|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/fast_tvb>>url:https://hub.docker.com/r/thevirtualbrain/fast_tvb]]
71 |=Download Page|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/fast_tvb>>url:https://hub.docker.com/r/thevirtualbrain/fast_tvb]]
72 |=License|GPL3
michaels 18.1 73 |=Current Version|1.0
74 |=All Versions|(((
75 * 1.0
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michaels 13.1 78
michaels 15.1 79 == Publications using TVB C ==
80
81 * [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/29308767>>url:https://www.ncbi.nlm.nih.gov/pubmed/29308767]]
82 * [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/32194282>>url:https://www.ncbi.nlm.nih.gov/pubmed/32194282]]
83 * [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/29911173>>url:https://www.ncbi.nlm.nih.gov/pubmed/29911173]]
84 * [[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]]
85 * [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/?term=31316116>>url:https://www.ncbi.nlm.nih.gov/pubmed/?term=31316116]]
86 * [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/?term=30035018>>url:https://www.ncbi.nlm.nih.gov/pubmed/?term=30035018]]
87 * [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/?term=27041212>>url:https://www.ncbi.nlm.nih.gov/pubmed/?term=27041212]]
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93 {{box title="**Contents**"}}
94 {{toc/}}
95 {{/box}}
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