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 68.1
edited by teodoramisan
on 2026/02/12 11:30
Change comment: There is no comment for this version

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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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164 164  === 1. Full TVB Simulation workflow ===
165 165  )))
166 166  
167 -Contains all TVB components necessary for running a TVB simulation (e.g., connectivity, coupling, model, integrator, monitor, simulator).
167 +Contains all TVB components necessary for running a TVB simulation (i.e. connectivity, coupling, model, integrator, monitor, simulator).
168 168  
169 169  {{html}}
170 170  <iframe width="1280" height="720" src="https://www.youtube.com/embed/bmqPlIJsWLk" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
171 171  {{/html}}
172 172  
173 -=== 2. Full VBI Inference workflow ===
174 174  
175 -Contains all VBI components required to run an inference workflow (e.g., inference configuration, model, simulator, train posterior, sample posterior).
174 +=== 2. Configuring model parameters using the PhasePlaneWidget: ===
176 176  
177 -[[image:vbi_workflow.png||height="590" width="1100"]]
178 -
179 -=== 3. Configuring model parameters using the PhasePlaneWidget: ===
180 -
181 181  Same workflow as before, but the parameter for the model used in simulation are set using the PhasePlaneWidget.
182 182  
183 183  {{html}}
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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  
187 -=== 4. Using siibra to retrieve connectivities from the EBRAINS KG ===
188 188  
183 +=== 3. Using siibra to retrieve connectivities from the EBRAINS KG ===
184 +
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.
190 190  
191 191  {{html}}
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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  
195 -=== 5. Run a workflow as an HPB job ===
196 196  
192 +=== 4. Run a workflow as an HPB job ===
193 +
197 197  A workflow simulation which is run remotely, by submitting a job to an HPC site and getting back the results (TimeSeries object).
198 198  
199 199  {{html}}<iframe width="1280" height="720" src="https://www.youtube.com/embed/M6rZClFgRrM" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>{{/html}}
vbi_workflow.png
Author
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1 -XWiki.teodoramisan
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TVB Widgets