Warning:  The Collaboratory IAM will be down today, April 24th from 17:30 (my timezone) for up to 2 minutes for an update. This will affect all services that require a log in.


Changes for page The Virtual Brain (TVB)

Last modified by ldomide on 2024/05/20 08:54
From version 44.1
edited by ldomide
on 2024/05/20 08:53
Change comment: There is no comment for this version
To version 27.1
edited by ldomide
on 2020/08/16 13:47
Change comment: There is no comment for this version

Summary

Details

Page properties
Content
... ... @@ -6,8 +6,6 @@
6 6  
7 7  
8 8  Lead Institutions: AIX Marseille University, Baycrest, Charité University Medicine Berlin
9 -
10 -Code maintainers: Codemart
11 11  )))
12 12  )))
13 13  
... ... @@ -21,16 +21,9 @@
21 21  (% class="wikigeneratedid" %)
22 22  //TheVirtualBrain// simulates and generates the time courses of various forms of neural activity including Local Field Potentials (LFP) and firing rate, as well as brain imaging data such as EEG, MEG and BOLD activations as observed in fMRI.
23 23  
24 -=== TVB-EBRAINS integrated workflows ===
25 -
26 -=== [[image:tvb-ebrain-diagram||alt="TVB-EBRAINS integrated workflows"]] ===
27 -
28 -(% class="wikigeneratedid" id="HFigure1:A0TVBatEBRAINScloudinfrastructure.Brainsimulationandneuroimagingworkflowsrequirepersonalmedicaldatathatisapplicabletodataprotectionregulation.Toprotectpersonaldatatheservicesrelyonend-to-endencryptionandaccesscontrol.EBRAINSprovidesseveralcoreservices:27Drive27isaserviceforhostingandsharingfiles3B27Wiki27and27Office27allowtocreateworkspacesanddocumentsforcollaborativeresearch3B27Lab27hostssandboxedJupyterLabinstancesforrunninglivecode3B27OpenShift27orchestratesdifferentservicesandprovidesresourcesforinteractivecomputing3B27HPC27aresupercomputingbackendsforresource-intensivecomputations.CoreservicesinteractwiththedifferentdeploymentsofTVBservicesviaaRESTfulAPIandUnicoreforcommunicationwithsupercomputers.TVBservicesaredeployedintheformofaWebGUI2Ccontainerimages2CPythonnotebooks2CPythonlibrariesandhigh-performancebackendcodes.TheTVBProcessingPipelineproducesstructuralandfunctionalconnectomesfromMRIdataanditsoutputscanbeingestedbyKnowledgeGraphandannotatedwithopenMINDSmetadata2Cwhichallowsre-usingtheconnectomesinotherservices.Theconnectorsshowinteractionsbetweendifferentcomponents28coloursgroupconnectorsfordifferentdeployments29." %)
29 -(% class="small" %)//TVB at EBRAINS cloud infrastructure. Brain simulation and neuroimaging workflows require personal medical data that is applicable to data protection regulation. To protect personal data the services rely on end-to-end encryption and access control. EBRAINS provides several core services: 'Drive' is a service for hosting and sharing files; 'Wiki' and 'Office' allow to create workspaces and documents for collaborative research; 'Lab' hosts sandboxed JupyterLab instances for running live code; 'OpenShift' orchestrates different services and provides resources for interactive computing; 'HPC' are supercomputing backends for resource-intensive computations. Core services interact with the different deployments of TVB services via a RESTful API and Unicore for communication with supercomputers. TVB services are deployed in the form of a Web GUI, container images, Python notebooks, Python libraries and high-performance backend codes. The TVB Processing Pipeline produces structural and functional connectomes from MRI data and its outputs can be ingested by KnowledgeGraph and annotated with openMINDS metadata, which allows re-using the connectomes in other services. The connectors show interactions between different components (colours group connectors for different deployments).//
30 -
31 31  === Quick links ===
32 32  
33 -* EBRAINS User Story for TVB: [[https:~~/~~/wiki.ebrains.eu/bin/view/Collabs/user-story-tvb/>>url:https://wiki.ebrains.eu/bin/view/Collabs/user-story-tvb/]]
24 +* HBP User Story for TVB: [[https:~~/~~/wiki.ebrains.eu/bin/view/Collabs/user-story-tvb/>>url:https://wiki.ebrains.eu/bin/view/Collabs/user-story-tvb/]]
34 34  * Main TVB web site: [[https:~~/~~/www.thevirtualbrain.org/>>url:https://www.thevirtualbrain.org/tvb/zwei]]
35 35  * Technical documentation for TVB is here: [[https:~~/~~/docs.thevirtualbrain.org/>>url:https://docs.thevirtualbrain.org/]]
36 36  * README about the current content: [[https:~~/~~/drive.ebrains.eu/f/7c83e516063a43c7b022/>>https://drive.ebrains.eu/f/7c83e516063a43c7b022/]]
... ... @@ -42,18 +42,12 @@
42 42  * TVB is open source, GPLv3 licensed:  [[https:~~/~~/github.com/the-virtual-brain>>url:https://github.com/the-virtual-brain]] so you can use it locally freely
43 43  * Within HBP infrastructure you will only need an HBP account to access TVB
44 44  
45 -== [[TVB CORE>>doc:.TVB Simulator Library.WebHome||target="_self"]]  [[image:https://www.thevirtualbrain.org/tvb/img/122412/zoom_landscape@2x||alt="ViewBrainActivity.jpg" height="177" width="283"]] ==
36 +== [[TVB CORE>>doc:.TVB Simulator Library.WebHome||target="_self"]]  [[image:https://www.thevirtualbrain.org/tvb/img/122412/zoom_landscape@2x||alt="ViewBrainActivity.jpg" height="177" width="283"]] ==
46 46  
47 -== [[TVB Multiscale>>doc:Collabs.the-virtual-brain-multiscale.WebHome||target="_self"]]  {{html}}<iframe width="302" height="170" src="https://www.youtube.com/embed/6hEuvxD7IDk?list=PLVtblERyzDeLcVv4BbW3BvmO8D-qVZxKf" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>{{/html}} ==
48 -
49 -== [[TVB Fast>>doc:Collabs.fast-tvb.WebHome]]  [[image:https://wiki.ebrains.eu/bin/download/Collabs/fast-tvb/WebHome/fast_tvb.png||alt="fast_tvb.png" height="147" width="281"]] ==
50 -
51 -== [[TVB Processing Pipeline>>doc:Collabs.tvb-pipeline.WebHome]] [[image:https://wiki.ebrains.eu/bin/download/Collabs/tvb-pipeline/WebHome/8677353.png||alt="8677353.png" height="214" width="214"]] ==
52 -
53 -
54 -== [[TVB Didactic Use Cases>>https://wiki.ebrains.eu/bin/view/Collabs/the-virtual-brain/TVB%20Didactic%20Use%20Cases/]] [[image:ipy_notebook_open.png||width="281"]] ==
38 +== [[TVB Multiscale>>doc:.TVB with NEST.WebHome||target="_self"]] {{html}}<iframe width="302" height="170" src="https://www.youtube.com/embed/6hEuvxD7IDk?list=PLVtblERyzDeLcVv4BbW3BvmO8D-qVZxKf" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>{{/html}} ==
55 55  )))
56 56  
41 +
57 57  (% class="col-xs-12 col-sm-4" %)
58 58  (((
59 59  {{box title="**Contents**"}}
... ... @@ -60,6 +60,6 @@
60 60  {{toc/}}
61 61  {{/box}}
62 62  
63 -== ==
48 +
64 64  )))
65 65  )))
Screen Shot 2020-09-28 at 2.56.22 PM (2).png
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.paulapopa
Size
... ... @@ -1,1 +1,0 @@
1 -196.4 KB
Content
ipy_notebook_open.png
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.paulapopa
Size
... ... @@ -1,1 +1,0 @@
1 -46.9 KB
Content
tvb-ebrain-diagram
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.paulapopa
Size
... ... @@ -1,1 +1,0 @@
1 -448.7 KB
Content
Collaboratory.Apps.Collab.Code.CollabClass[0]
owner
... ... @@ -1,1 +1,0 @@
1 -ldomide
XWiki.XWikiRights[7]
Allow/Deny
... ... @@ -1,1 +1,0 @@
1 -Allow
Levels
... ... @@ -1,1 +1,0 @@
1 -view
Users
... ... @@ -1,1 +1,0 @@
1 -XWiki.XWikiGuest
XWiki.XWikiRights[8]
Allow/Deny
... ... @@ -1,1 +1,0 @@
1 -Allow
Groups
... ... @@ -1,1 +1,0 @@
1 -XWiki.XWikiAllGroup
Levels
... ... @@ -1,1 +1,0 @@
1 -view
XWiki.XWikiRights[5]
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[6]
Allow/Deny
... ... @@ -1,0 +1,1 @@
1 +Allow
Groups
... ... @@ -1,0 +1,1 @@
1 +XWiki.XWikiAllGroup
Levels
... ... @@ -1,0 +1,1 @@
1 +view