Last modified by teodoramisan on 2026/02/13 10:11
From version 73.4
edited by teodoramisan
on 2026/02/13 09:16
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

Summary

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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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156 156  
157 157  [[image:timeseries-plotly.png||alt="view3.png" height="593" width="1100"]]
158 158  
159 -=== 3. Visualize posterior pairplot resulted from an inference workflow ===
160 -
161 -This functionality is available for the SamplePosterior component. Right click on the component and select the Open Viewer functionality.
162 -
163 -This opens a new JupyterLab tab with an editable notebook. After following the instructions in the notebook, you will generate a pairplot of the posterior samples, showing the distribution of each parameter (uncertainty) and the relationships between parameters.
164 -
165 -*Make sure the workflow has been executed so the viewer has data to load.
166 -
167 167  == ==
168 168  
169 169  == Workflow examples ==
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172 172  === 1. Full TVB Simulation workflow ===
173 173  )))
174 174  
175 -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).
176 176  
177 177  {{html}}
178 178  <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>
179 179  {{/html}}
180 180  
181 -=== 2. Full VBI Inference workflow ===
182 182  
183 -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: ===
184 184  
185 -[[image:vbi_workflow.png||height="590" width="1100"]]
186 -
187 -=== 3. Configuring model parameters using the PhasePlaneWidget: ===
188 -
189 189  Same workflow as before, but the parameter for the model used in simulation are set using the PhasePlaneWidget.
190 190  
191 191  {{html}}
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192 192  <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>
193 193  {{/html}}
194 194  
195 -=== 4. Using siibra to retrieve connectivities from the EBRAINS KG ===
196 196  
183 +=== 3. Using siibra to retrieve connectivities from the EBRAINS KG ===
184 +
197 197  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.
198 198  
199 199  {{html}}
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200 200  <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>
201 201  {{/html}}
202 202  
203 -=== 5. Run a workflow as an HPB job ===
204 204  
192 +=== 4. Run a workflow as an HPB job ===
193 +
205 205  A workflow simulation which is run remotely, by submitting a job to an HPC site and getting back the results (TimeSeries object).
206 206  
207 207  {{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