Last modified by michaels on 2022/05/23 22:24
From version 6.1
edited by michaels
on 2020/05/04 16:02
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To version 22.1
edited by michaels
on 2020/07/28 18:04
Change comment: There is no comment for this version

Summary

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1 +tool|CHARITE|brain network model|brain simulation|tvb|high performance|parallel|hpc|supercomputer|connectome|functional connectivity|the virtual brain
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2 2  (((
3 3  (% class="container" %)
4 4  (((
5 -= My Collab's Extended Title =
5 += TVB C ~-~- High-speed parallel brain network models =
6 6  
7 -My collab's subtitle
7 +A fast implementation of The Virtual Brain brain network simulator
8 +
9 +[[Direct link to notebook>>https://drive.ebrains.eu/#my-libs/lib/f5e40b3b-91cb-4671-9178-4d2673ad8ac4]]
10 +
11 +[[image:4144.jpeg]]
8 8  )))
9 9  )))
10 10  
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12 12  (((
13 13  (% class="col-xs-12 col-sm-8" %)
14 14  (((
15 -= What can I find here? =
19 +== Quick links ==
16 16  
17 -* Notice how the table of contents on the right
18 -* is automatically updated
19 -* to hold this page's headers
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"]]
20 20  
21 -= Who has access? =
26 +== What can I find here? ==
22 22  
23 -Describe the audience of this collab.
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]]
24 24  )))
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
75 +)))
76 +)))
25 25  
78 +== Publications using TVB C ==
26 26  
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]]
87 +)))
88 +
89 +
27 27  (% class="col-xs-12 col-sm-4" %)
28 28  (((
29 29  {{box title="**Contents**"}}
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