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-= My Collab's Extended Title = |
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+= High-speed parallel brain network simulation = |
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-My collab's subtitle |
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+A fast implementation of The Virtual Brain brain network simulator |
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-= What can I find here? = |
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+[[Direct link to notebook>>url:https://drive.ebrains.eu/#my-libs/lib/f5e40b3b-91cb-4671-9178-4d2673ad8ac4]] |
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-* Notice how the table of contents on the right |
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-* is automatically updated |
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-* to hold this page's headers |
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+[[image:4144.jpeg]] |
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-= Who has access? = |
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+== Quick links == |
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-Describe the audience of this collab. |
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+* [[TVB on EBRAINS (Short Version)>>url:https://www.youtube.com/watch?v=_G_DjRb1ams&feature=youtu.be]] |
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+* [[TVB on EBRAINS (Long Version)>>url:https://www.youtube.com/watch?v=eZrh6ztGFAY&feature=youtu.be]] |
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+* [[TVB on EBRAINS (Mini Videos)>>url:https://www.youtube.com/playlist?list=PLVtblERyzDeLcVv4BbW3BvmO8D-qVZxKf]] |
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+* [[User Story>>url:https://wiki.ebrains.eu/bin/view/Collabs/user-story-tvb/]] |
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+ |
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+== What can I find here? == |
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+ |
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+* an IPython notebook that describes how to |
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+** pull the TVB-C container into one of the associated supercomputers using PyUnicore |
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+** upload model data to the supercomputer |
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+** set up and run simulations |
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+** download simulation results |
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+ |
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+== How do I use it? == |
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+ |
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+* the simulation code is implemented as a Docker container |
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+* the container is executed on supercomputers and operated via IPython notebooks |
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+* Find the notebook by clicking on "Drive" in the left menu. The notebook is called "TVB_C.ipynb" |
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+* To use the notebook, download it onto your local filesystem, create a new Collab and upload it there. |
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+* Then, head over to [[https:~~/~~/lab.ebrains.eu/>>url:https://lab.ebrains.eu/]] to edit and run your notebook. |
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+* 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'" |
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+ |
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+== Metadata == |
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+ |
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+|=((( |
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+|=Category|tool |
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+|=Tags|((( |
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+* [[brain-network-model>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]] |
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+* [[TVB>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]] |
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+* [[high-performance>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]] |
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+* [[parallel>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]] |
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+* [[HPC>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]] |
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+* [[supercomputer>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]] |
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+* [[brain-simulation>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]] |
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+* [[connectome>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]] |
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+* [[functional-connectivity>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]] |
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+* [[The-Virtual-Brain>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]] |
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))) |
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+|=Partners|((( |
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+* Charité Universitätsmedizin Berlin [[CHARITE>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]] |
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+))) |
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+|=Maintainers|((( |
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+* [[Petra Ritter>>path:mailto:petra.ritter@charite.de]] |
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+* [[Michael Schirner>>path:mailto:michael.schirner@charite.de]] |
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+))) |
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+|=Homepage|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/fast_tvb>>url:https://hub.docker.com/r/thevirtualbrain/fast_tvb]] |
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+|=Documentation|[[https:~~/~~/collab.humanbrainproject.eu/#/collab/65304/nav/444404>>url:https://collab.humanbrainproject.eu/#/collab/65304/nav/444404]] |
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+|=Support|[[michael.schirner@charite.de>>path:mailto:michael.schirner@charite.de]] |
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+|=Source Code|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/fast_tvb>>url:https://hub.docker.com/r/thevirtualbrain/fast_tvb]] |
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+|=Download Page|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/fast_tvb>>url:https://hub.docker.com/r/thevirtualbrain/fast_tvb]] |
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+|=License|GPL3 |
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+|=Current Version|1.0 |
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+|=All Versions|((( |
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+* 1.0 |
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+))) |
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+))) |
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+== Publications using TVB C == |
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+* [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/29308767>>url:https://www.ncbi.nlm.nih.gov/pubmed/29308767]] |
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+* [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/32194282>>url:https://www.ncbi.nlm.nih.gov/pubmed/32194282]] |
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+* [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/29911173>>url:https://www.ncbi.nlm.nih.gov/pubmed/29911173]] |
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+* [[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]] |
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+* [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/?term=31316116>>url:https://www.ncbi.nlm.nih.gov/pubmed/?term=31316116]] |
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+* [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/?term=30035018>>url:https://www.ncbi.nlm.nih.gov/pubmed/?term=30035018]] |
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+* [[https:~~/~~/www.ncbi.nlm.nih.gov/pubmed/?term=27041212>>url:https://www.ncbi.nlm.nih.gov/pubmed/?term=27041212]] |
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+ |
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{{box title="**Contents**"}} |
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{{toc/}} |
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{{/box}} |
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