Last modified by michaels on 2022/05/23 22:24
From version 4.1
edited by michaels
on 2020/05/04 16:02
Change comment: There is no comment for this version
To version 19.1
edited by michaels
on 2020/05/06 15:08
Change comment: There is no comment for this version

Summary

Details

Page properties
Tags
... ... @@ -1,0 +1,1 @@
1 +tool|CHARITE|brain network model|brain simulation|tvb|high performance|parallel|hpc|supercomputer|connectome|functional connectivity|the virtual brain
Content
... ... @@ -2,9 +2,13 @@
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  
... ... @@ -12,18 +12,70 @@
12 12  (((
13 13  (% class="col-xs-12 col-sm-8" %)
14 14  (((
15 -= What can I find here? =
19 +== What can I find here? ==
16 16  
17 -* Notice how the table of contents on the right
18 -* is automatically updated
19 -* to hold this page's headers
21 +* an IPython notebook that describes how to
22 +** pull the TVB-C container into one of the associated supercomputers using PyUnicore
23 +** upload model data to the supercomputer
24 +** set up and run simulations
25 +** download simulation results
20 20  
21 -= Who has access? =
27 +== How do I use it? ==
22 22  
23 -Describe the audience of this collab.
29 +* the simulation code is implemented as a Docker container
30 +* the container is executed on supercomputers and operated via IPython notebooks
31 +* Find the notebook by clicking on "Drive" in the left menu. The notebook is called "TVB_C.ipynb"
32 +* To use the notebook, download it onto your local filesystem, create a new Collab and upload it there.
33 +* Then, head over to [[https:~~/~~/lab.ebrains.eu/>>url:https://lab.ebrains.eu/]] to edit and run your notebook.
34 +* 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'"
35 +
36 +== Metadata ==
37 +
38 +|=(((
39 +|=Category|tool
40 +|=Tags|(((
41 +* [[brain-network-model>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
42 +* [[TVB>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
43 +* [[high-performance>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
44 +* [[parallel>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
45 +* [[HPC>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
46 +* [[supercomputer>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
47 +* [[brain-simulation>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
48 +* [[connectome>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
49 +* [[functional-connectivity>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
50 +* [[The-Virtual-Brain>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
24 24  )))
52 +|=Partners|(((
53 +* Charité Universitätsmedizin Berlin [[CHARITE>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]
54 +)))
55 +|=Maintainers|(((
56 +* [[Petra Ritter>>path:mailto:petra.ritter@charite.de]]
57 +* [[Michael Schirner>>path:mailto:michael.schirner@charite.de]]
58 +)))
59 +|=Homepage|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/fast_tvb>>url:https://hub.docker.com/r/thevirtualbrain/fast_tvb]]
60 +|=Documentation|[[https:~~/~~/collab.humanbrainproject.eu/#/collab/65304/nav/444404>>url:https://collab.humanbrainproject.eu/#/collab/65304/nav/444404]]
61 +|=Support|[[michael.schirner@charite.de>>path:mailto:michael.schirner@charite.de]]
62 +|=Source Code|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/fast_tvb>>url:https://hub.docker.com/r/thevirtualbrain/fast_tvb]]
63 +|=Download Page|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/fast_tvb>>url:https://hub.docker.com/r/thevirtualbrain/fast_tvb]]
64 +|=License|GPL3
65 +|=Current Version|1.0
66 +|=All Versions|(((
67 +* 1.0
68 +)))
69 +)))
25 25  
71 +== Publications using TVB C ==
26 26  
73 +* [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/29308767>>url:https://www.ncbi.nlm.nih.gov/pubmed/29308767]]
74 +* [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/32194282>>url:https://www.ncbi.nlm.nih.gov/pubmed/32194282]]
75 +* [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/29911173>>url:https://www.ncbi.nlm.nih.gov/pubmed/29911173]]
76 +* [[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]]
77 +* [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/?term=31316116>>url:https://www.ncbi.nlm.nih.gov/pubmed/?term=31316116]]
78 +* [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/?term=30035018>>url:https://www.ncbi.nlm.nih.gov/pubmed/?term=30035018]]
79 +* [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/?term=27041212>>url:https://www.ncbi.nlm.nih.gov/pubmed/?term=27041212]]
80 +)))
81 +
82 +
27 27  (% class="col-xs-12 col-sm-4" %)
28 28  (((
29 29  {{box title="**Contents**"}}
4144.jpeg
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.michaels
Size
... ... @@ -1,0 +1,1 @@
1 +146.3 KB
Content
fasttvb.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.michaels
Size
... ... @@ -1,0 +1,1 @@
1 +36.4 KB
Content
XWiki.XWikiRights[3]
Allow/Deny
... ... @@ -1,0 +1,1 @@
1 +Allow
Levels
... ... @@ -1,0 +1,1 @@
1 +view
Users
... ... @@ -1,0 +1,1 @@
1 +XWiki.XWikiGuest
XWiki.XWikiRights[4]
Allow/Deny
... ... @@ -1,0 +1,1 @@
1 +Allow
Groups
... ... @@ -1,0 +1,1 @@
1 +XWiki.XWikiAllGroup
Levels
... ... @@ -1,0 +1,1 @@
1 +view