Changes for page The Virtual Brain (TVB)

Last modified by ldomide on 2024/05/20 08:54
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edited by paulapopa
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1 -The Virtual Brain (TVB)
1 +The Virtual Brain
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1 -XWiki.paulapopa
1 +XWiki.ldomide
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2 2  (((
3 3  (% class="container" %)
4 4  (((
5 -= The Virtual Brain  [[image:1591110520091-521.png]] =
5 += My Collab's Extended Title =
6 6  
7 -
8 -Lead Institutions: AIX Marseille University, Baycrest, Charité University Medicine Berlin
7 +My collab's subtitle
9 9  )))
10 10  )))
11 11  
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13 13  (((
14 14  (% class="col-xs-12 col-sm-8" %)
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17 -//TheVirtualBrain// is a framework for the simulation of the dynamics of large-scale brain networks with biologically realistic connectivity. //TheVirtualBrain// uses tractographic data (DTI/DSI) to generate connectivity matrices and build cortical and subcortical brain networks. The connectivity matrix defines the connection strengths and time delays via signal transmission between all network nodes. Various neural mass models are available in the repertoire of //TheVirtualBrain// and define the dynamics of a network node. Together, the neural mass models at the network nodes and the connectivity matrix define **the Virtual Brain**.
15 += What can I find here? =
18 18  
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20 -//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.
17 +* Notice how the table of contents on the right
18 +* is automatically updated
19 +* to hold this page's headers
21 21  
22 -=== TVB-EBRAINS integrated workflows ===
21 += Who has access? =
23 23  
24 -=== [[image:tvb-ebrain-diagram||alt="TVB-EBRAINS integrated workflows"]] ===
25 -
26 -(% class="wikigeneratedid" id="HFigure1:A0TVBatEBRAINScloudinfrastructure.Brainsimulationandneuroimagingworkflowsrequirepersonalmedicaldatathatisapplicabletodataprotectionregulation.Toprotectpersonaldatatheservicesrelyonend-to-endencryptionandaccesscontrol.EBRAINSprovidesseveralcoreservices:27Drive27isaserviceforhostingandsharingfiles3B27Wiki27and27Office27allowtocreateworkspacesanddocumentsforcollaborativeresearch3B27Lab27hostssandboxedJupyterLabinstancesforrunninglivecode3B27OpenShift27orchestratesdifferentservicesandprovidesresourcesforinteractivecomputing3B27HPC27aresupercomputingbackendsforresource-intensivecomputations.CoreservicesinteractwiththedifferentdeploymentsofTVBservicesviaaRESTfulAPIandUnicoreforcommunicationwithsupercomputers.TVBservicesaredeployedintheformofaWebGUI2Ccontainerimages2CPythonnotebooks2CPythonlibrariesandhigh-performancebackendcodes.TheTVBProcessingPipelineproducesstructuralandfunctionalconnectomesfromMRIdataanditsoutputscanbeingestedbyKnowledgeGraphandannotatedwithopenMINDSmetadata2Cwhichallowsre-usingtheconnectomesinotherservices.Theconnectorsshowinteractionsbetweendifferentcomponents28coloursgroupconnectorsfordifferentdeployments29." %)
27 -(% 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).//
28 -
29 -=== Quick links ===
30 -
31 -* 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/]]
32 -* Main TVB web site: [[https:~~/~~/www.thevirtualbrain.org/>>url:https://www.thevirtualbrain.org/tvb/zwei]]
33 -* Technical documentation for TVB is here: [[https:~~/~~/docs.thevirtualbrain.org/>>url:https://docs.thevirtualbrain.org/]]
34 -* README about the current content: [[https:~~/~~/drive.ebrains.eu/f/7c83e516063a43c7b022/>>https://drive.ebrains.eu/f/7c83e516063a43c7b022/]]
35 -* Code authors: [[https:~~/~~/raw.githubusercontent.com/the-virtual-brain/tvb-root/master/framework_tvb/AUTHORS>>url:https://raw.githubusercontent.com/the-virtual-brain/tvb-root/master/framework_tvb/AUTHORS]]
36 -* Contact us at [[https:~~/~~/groups.google.com/group/tvb-users/>>url:https://groups.google.com/group/tvb-users/]]
37 -
38 -=== Who has access? ===
39 -
40 -* 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
41 -* Within HBP infrastructure you will only need an HBP account to access TVB
42 -
43 -== [[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"]] ==
44 -
45 -== [[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}} ==
46 -
47 -== [[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"]] ==
48 -
49 -== [[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"]] ==
50 -
51 -
52 -== [[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"]] ==
23 +Describe the audience of this collab.
53 53  )))
54 54  
26 +
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56 56  (((
57 57  {{box title="**Contents**"}}
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58 58  {{toc/}}
59 59  {{/box}}
60 60  
61 -== ==
33 +
62 62  )))
63 63  )))
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1 -TVB (The Virtual Brain) core software packages in HBP Collab.
2 -TVB simulator in combination with NEST for a multiscale co-simulation.
3 -TVB Full Brain Modeling. Human. Animal. EEG, MEG, SEEG, iEEG, BOLD.
4 -Large Scale Connectivity. Region and Surface level Simulations.
1 +Tutorial for configuring and launching simulations with TVB software package from HBP Collab.
2 +We even have a section for using TVB simulator in combination with NEST simulator, and do a co-simulation
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