Wiki source code of Fast_TVB

Version 9.1 by michaels on 2020/07/08 16:12
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michaels 8.1 5 = High-speed parallel brain network simulation =
michaels 1.1 6
michaels 7.1 7 A fast implementation of The Virtual Brain brain network simulator
michaels 1.1 8
michaels 7.1 9 [[Direct link to notebook>>url:https://drive.ebrains.eu/#my-libs/lib/f5e40b3b-91cb-4671-9178-4d2673ad8ac4]]
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michaels 7.1 11 [[image:4144.jpeg]]
michaels 1.1 12
michaels 7.1 13 == Quick links ==
michaels 1.1 14
michaels 7.1 15 * [[TVB on EBRAINS (Short Version)>>url:https://www.youtube.com/watch?v=_G_DjRb1ams&feature=youtu.be]]
16 * [[TVB on EBRAINS (Long Version)>>url:https://www.youtube.com/watch?v=eZrh6ztGFAY&feature=youtu.be]]
17 * [[TVB on EBRAINS (Mini Videos)>>url:https://www.youtube.com/playlist?list=PLVtblERyzDeLcVv4BbW3BvmO8D-qVZxKf]]
18 * [[User Story>>url:https://wiki.ebrains.eu/bin/view/Collabs/user-story-tvb/]]
19
20 == What can I find here? ==
21
22 * an IPython notebook that describes how to
23 ** pull the TVB-C container into one of the associated supercomputers using PyUnicore
24 ** upload model data to the supercomputer
25 ** set up and run simulations
26 ** download simulation results
27
28 == How do I use it? ==
29
30 * the simulation code is implemented as a Docker container
31 * the container is executed on supercomputers and operated via IPython notebooks
32 * Find the notebook by clicking on "Drive" in the left menu. The notebook is called "TVB_C.ipynb"
33 * To use the notebook, download it onto your local filesystem, create a new Collab and upload it there.
34 * Then, head over to [[https:~~/~~/lab.ebrains.eu/>>url:https://lab.ebrains.eu/]] to edit and run your notebook.
35 * 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'"
36
37 == Metadata ==
38
39 |=(((
40 |=Category|tool
41 |=Tags|(((
42 * [[brain-network-model>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
43 * [[TVB>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
44 * [[high-performance>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
45 * [[parallel>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
46 * [[HPC>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
47 * [[supercomputer>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
48 * [[brain-simulation>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
49 * [[connectome>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
50 * [[functional-connectivity>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
51 * [[The-Virtual-Brain>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
michaels 1.1 52 )))
michaels 7.1 53 |=Partners|(((
54 * Charité Universitätsmedizin Berlin [[CHARITE>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
55 )))
56 |=Maintainers|(((
57 * [[Petra Ritter>>path:mailto:petra.ritter@charite.de]]
58 * [[Michael Schirner>>path:mailto:michael.schirner@charite.de]]
59 )))
60 |=Homepage|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/fast_tvb>>url:https://hub.docker.com/r/thevirtualbrain/fast_tvb]]
61 |=Documentation|[[https:~~/~~/collab.humanbrainproject.eu/#/collab/65304/nav/444404>>url:https://collab.humanbrainproject.eu/#/collab/65304/nav/444404]]
62 |=Support|[[michael.schirner@charite.de>>path:mailto:michael.schirner@charite.de]]
63 |=Source Code|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/fast_tvb>>url:https://hub.docker.com/r/thevirtualbrain/fast_tvb]]
64 |=Download Page|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/fast_tvb>>url:https://hub.docker.com/r/thevirtualbrain/fast_tvb]]
65 |=License|GPL3
66 |=Current Version|1.0
67 |=All Versions|(((
68 * 1.0
69 )))
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michaels 1.1 71
michaels 7.1 72 == Publications using TVB C ==
michaels 1.1 73
michaels 7.1 74 * [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/29308767>>url:https://www.ncbi.nlm.nih.gov/pubmed/29308767]]
75 * [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/32194282>>url:https://www.ncbi.nlm.nih.gov/pubmed/32194282]]
76 * [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/29911173>>url:https://www.ncbi.nlm.nih.gov/pubmed/29911173]]
77 * [[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]]
78 * [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/?term=31316116>>url:https://www.ncbi.nlm.nih.gov/pubmed/?term=31316116]]
79 * [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/?term=30035018>>url:https://www.ncbi.nlm.nih.gov/pubmed/?term=30035018]]
80 * [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/?term=27041212>>url:https://www.ncbi.nlm.nih.gov/pubmed/?term=27041212]]
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michaels 1.1 82 {{box title="**Contents**"}}
83 {{toc/}}
84 {{/box}}
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