Last modified by teodoramisan on 2026/02/13 10:11
From version 77.1
edited by teodoramisan
on 2026/02/13 09:33
Change comment: There is no comment for this version
To version 67.1
edited by teodoramisan
on 2026/02/12 11:27
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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61 61  
62 62  The components that are provided in this extensions are configurable, meaning you can set some parameters on almost every component. Some of the parameters are literals, while some parameters are results of other components.
63 63  
64 -Parameters marked with a star (★) are mandatory, the workflow will not run until all required parameters have values assigned.
64 +Parameters marked with a star (*) are mandatory, the workflow will not run until all required parameters have values assigned.
65 65  
66 66  In case of primitives you need to open the //General// tab from the components tray and drag the appropriate //literal//: float, int, string, dict, etc.
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 -
160 -=== 3. Visualize posterior samples with a pairplot (VBI inferenece) ===
161 -
162 -This functionality is available for the **SamplePosterior** component. Right click on the component and select the **Open Viewer** functionality.
163 -
164 -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.
165 -
166 -*Make sure the workflow has been executed so the viewer has data to load.
167 -
168 -[[image:plot-posteriors.png||height="593" width="1100"]]
169 -
170 -
171 -=== 4. Visualize time series from VBI simulations ===
172 -
173 -This functionality is available for the **SimulationRunner** component. Right click on the component and select the **Open Viewer** functionality.
174 -
175 -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.
176 -
177 -*Make sure the workflow has been executed so the viewer has data to load.
178 -[[image:plot-timeseries-vbi.png||height="592" width="1100"]]
179 -
180 180  == ==
181 181  
182 182  == Workflow examples ==
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185 185  === 1. Full TVB Simulation workflow ===
186 186  )))
187 187  
188 -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).
189 189  
190 190  {{html}}
191 191  <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>
192 192  {{/html}}
193 193  
194 -=== 2. Full VBI Inference workflow ===
195 195  
196 -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: ===
197 197  
198 -[[image:vbi_workflow.png||height="590" width="1100"]]
199 -
200 -=== 3. Configuring model parameters using the PhasePlaneWidget: ===
201 -
202 202  Same workflow as before, but the parameter for the model used in simulation are set using the PhasePlaneWidget.
203 203  
204 204  {{html}}
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205 205  <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>
206 206  {{/html}}
207 207  
208 -=== 4. Using siibra to retrieve connectivities from the EBRAINS KG ===
209 209  
183 +=== 3. Using siibra to retrieve connectivities from the EBRAINS KG ===
184 +
210 210  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.
211 211  
212 212  {{html}}
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213 213  <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>
214 214  {{/html}}
215 215  
216 -=== 5. Run a workflow as an HPB job ===
217 217  
192 +=== 4. Run a workflow as an HPB job ===
193 +
218 218  A workflow simulation which is run remotely, by submitting a job to an HPC site and getting back the results (TimeSeries object).
219 219  
220 -=== 6. Parallel simulations workflow ===
221 -
222 -This example demonstrates **Parameter Space Exploration** (PSE) by running multiple TVB simulations in parallel for different parameter combinations.
223 -
224 -The workflow uses two nested ForEach components to iterate over coupling and conduction speed sets of values. For each (coupling, conduction_speed) pair, a simulation run is executed with the help of the RunParallelProcess component, which runs the workflow body in separate worker processes (using multiprocessing + dill).
225 -
226 -[[image:parallel-simulations.png||height="590" width="1100"]]
227 -
228 -
229 229  {{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}}
230 230  
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TVB Widgets