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 35.1
edited by paulapopa
on 2020/10/19 10:21
Change comment: Uploaded new attachment "tvb-ebrain-diagram", version {1}

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8 8  Lead Institutions: AIX Marseille University, Baycrest, Charité University Medicine Berlin
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10 -Code maintainers: Codemart
11 11  )))
12 12  )))
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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"]] ===
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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/]]
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51 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 52  
53 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"]] ==
45 +== [[TVB Didactic Use Cases>>https://wiki.ebrains.eu/bin/view/Collabs/the-virtual-brain/TVB%20Didactic%20Use%20Cases/]] [[image:http://docs.thevirtualbrain.com/_images/ipy_notebook_open.png||height="147"]] ==
55 55  )))
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