Last modified by teodoramisan on 2026/02/13 10:11
From version 73.2
edited by teodoramisan
on 2026/02/13 09:13
Change comment: There is no comment for this version
To version 69.1
edited by teodoramisan
on 2026/02/12 11:50
Change comment: There is no comment for this version

Summary

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4 4  
5 5  This extension is also installed already in EBRAINS lab, where it can be tested directly.
6 6  
7 -== Jupyter Lab Extension for building and executing TVB and vBI Workflows on EBRAINS ==
7 +== Jupyter Lab Extension for building and executing TVB and VBI Workflows on EBRAINS ==
8 8  
9 9  == Purpose ==
10 10  
11 -This is a Jupyter Lab extension that offers graphical support for TVB and VBI workflows. It is already available in the EBRAINS Lab and it allows users to configure and execute TVB simulations and VBI inference workflows directly from a GUI, while drastically reducing the complexity of configuring them inside a Jupyter Lab notebook.
11 +This is a Jupyter Lab extension that offers graphical support for TVB and VBI workflows. It is already available in the EBRAINS Lab and it allows users to configure and execute TVB simulations and VBI inference workflows directly from a GUI, while drastically reducing the complexity of configuring them inside a Jupyter Lab notebook. Try edit
12 12  
13 13  {{html}}
14 14  <iframe width="1200" height="450" src="https://www.youtube.com/embed/-cjZOsU6PBg" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
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142 142  [[image:export-model-configuration.png||alt="image-20221116130425-1.png" data-xwiki-image-style-alignment="center" height="763" width="1000"]]
143 143  
144 144  
145 -=== 2. Visualize time series resulted from TVB simulations ===
145 +=== 2. Visualize time series resulted from simulations ===
146 146  
147 147  This functionality is available for the **StoreResultsToDrive** component. Right click on the **StoreResultsToDrive** and select the **Open Viewer** option:
148 148  
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176 176  
177 177  [[image:vbi_workflow.png||height="590" width="1100"]]
178 178  
179 +(% class="wikigeneratedid" %)
180 +{{{ }}}
181 +
182 +
179 179  === 3. Configuring model parameters using the PhasePlaneWidget: ===
180 180  
181 181  Same workflow as before, but the parameter for the model used in simulation are set using the PhasePlaneWidget.
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184 184  <iframe width="1280" height="720" src="https://www.youtube.com/embed/jhGfYul1z9k" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
185 185  {{/html}}
186 186  
191 +
187 187  === 4. Using siibra to retrieve connectivities from the EBRAINS KG ===
188 188  
189 189  A simulation workflow where **siibra **is used to retrieve a connectivity from the EBRAINS KG. That connectivity is fed into a TVB Simulator, where the rest of the parameters (coupling, model, etc.) are set to default values.
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192 192  <iframe width="1280" height="720" src="https://www.youtube.com/embed/hnqTpFGCYMg" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
193 193  {{/html}}
194 194  
200 +
195 195  === 5. Run a workflow as an HPB job ===
196 196  
197 197  A workflow simulation which is run remotely, by submitting a job to an HPC site and getting back the results (TimeSeries object).
Public

TVB Widgets