Last modified by teodoramisan on 2026/02/13 10:11
From version 73.6
edited by teodoramisan
on 2026/02/13 09:18
Change comment: There is no comment for this version
To version 67.2
edited by teodoramisan
on 2026/02/12 11:29
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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67 67  
68 68  The parameters need to be linked to the inputs of the component by dragging and dropping a connection from the output port of a literal/component towards the corresponding input port of the other component (e.g. the gray connections in the screenshot below).
69 69  
70 -Components and parameters include info buttons (**i**) that explain their purpose and how they are used (e.g. the simulator info panel below).
70 +Components and parameters include info buttons (i) that explain their purpose and how they are used (e.g. the simulator info panel below).
71 71  
72 72  [[image:Screenshot 2026-02-12 115445.png||alt="diagr.png" height="592" width="1100"]]
73 73  
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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 -[[image:plot-posteriors.png||height="593" width="1100"]]
168 -
169 -=== 4. Visualize time series resulted from VBI simulations ===
170 -
171 -This functionality is available for the SimulationRunner component. Right click on the component and select the Open Viewer functionality.
172 -
173 -This opens a new JupyterLab tab with an editable notebook. After following the instructions in the notebook, you will see a simple time-series plot of the simulated model signal over time.
174 -
175 -*Make sure the workflow has been executed so the viewer has data to load.
176 -[[image:plot-timeseries-vbi.png||height="592" width="1100"]]
177 -
178 178  == ==
179 179  
180 180  == Workflow examples ==
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183 183  === 1. Full TVB Simulation workflow ===
184 184  )))
185 185  
186 -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).
187 187  
188 188  {{html}}
189 189  <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>
190 190  {{/html}}
191 191  
192 -=== 2. Full VBI Inference workflow ===
193 193  
194 -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: ===
195 195  
196 -[[image:vbi_workflow.png||height="590" width="1100"]]
197 -
198 -=== 3. Configuring model parameters using the PhasePlaneWidget: ===
199 -
200 200  Same workflow as before, but the parameter for the model used in simulation are set using the PhasePlaneWidget.
201 201  
202 202  {{html}}
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203 203  <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>
204 204  {{/html}}
205 205  
206 -=== 4. Using siibra to retrieve connectivities from the EBRAINS KG ===
207 207  
183 +=== 3. Using siibra to retrieve connectivities from the EBRAINS KG ===
184 +
208 208  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.
209 209  
210 210  {{html}}
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211 211  <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>
212 212  {{/html}}
213 213  
214 -=== 5. Run a workflow as an HPB job ===
215 215  
192 +=== 4. Run a workflow as an HPB job ===
193 +
216 216  A workflow simulation which is run remotely, by submitting a job to an HPC site and getting back the results (TimeSeries object).
217 217  
218 218  {{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}}
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Public

TVB Widgets