Last modified by teodoramisan on 2026/02/13 10:11
From version 66.1
edited by teodoramisan
on 2026/02/12 11:25
Change comment: There is no comment for this version
To version 75.1
edited by teodoramisan
on 2026/02/13 09:23
Change comment: There is no comment for this version

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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. Try edit
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.
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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130 130  To use this functionality, drag any model from the **TVB_MODELS** (inside the components tray) into the workflow area. Then right click on the model and select the **Open Viewer** option:
131 131  
132 132  
133 -[[image:open-viewer-on-models.png||alt="image-20221116125354-2.png" data-xwiki-image-style-alignment="center" height="800" width="1130"]]
133 +[[image:open-viewer-on-models.png||alt="image-20221116125354-2.png" data-xwiki-image-style-alignment="center" height="593" width="1100"]]
134 134  
135 135  
136 136  A new Jupyter tab should open, which contains a read-only Jupyter notebook. After following the instructions provided there, you should be able to see the Phase Plane widget associated with this particular model.
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139 139  
140 140  After configuring the parameters with the desired values, go to the Exports tab of the widget and click on **Export model configuration**. Now all you have to do is to go back to the tab where your workflow is and you will see that the model will have values set for all the parameters that you modified in the Phase Plane widget (that is all the parameters there were assigned values different than the default ones).
141 141  
142 -[[image:export-model-configuration.png||alt="image-20221116130425-1.png" data-xwiki-image-style-alignment="center" height="900" width="1069"]]
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 simulations ===
145 +=== 2. Visualize time series resulted from TVB 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  
149 -[[image:open-viewer-button.png||alt="view.png"]]
149 +[[image:open-viewer-button.png||alt="view.png" height="591" width="1100"]]
150 150  
151 151  A new Jupyter tab should open, which contains a read-only Jupyter notebook. After running the cell, you should be able to see the **TimeSeriesBrowser **widget with the //**Collab**// and //**folder**// you have chosen for the **StoreResultsToDrive **component already loaded.
152 152  
153 -[[image:view2.png]]
153 +[[image:view2.png||height="576" width="1100"]]
154 154  
155 155  Next, you should choose which time series file to display and click the **View time series button**.
156 156  
157 -[[image:timeseries-plotly.png||alt="view3.png"]]
157 +[[image:timeseries-plotly.png||alt="view3.png" height="593" width="1100"]]
158 158  
159 +
160 +=== 3. Visualize posterior pairplot resulted from an inference workflow ===
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 resulted 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 +
159 159  == ==
160 160  
161 161  == Workflow examples ==
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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 (i.e. connectivity, coupling, model, integrator, monitor, simulator).
188 +Contains all TVB components necessary for running a TVB simulation (e.g., 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  
194 +=== 2. Full VBI Inference workflow ===
173 173  
174 -=== 2. Configuring model parameters using the PhasePlaneWidget: ===
196 +Contains all VBI components required to run an inference workflow (e.g., inference configuration, model, simulator, train posterior, sample posterior).
175 175  
198 +[[image:vbi_workflow.png||height="590" width="1100"]]
199 +
200 +=== 3. Configuring model parameters using the PhasePlaneWidget: ===
201 +
176 176  Same workflow as before, but the parameter for the model used in simulation are set using the PhasePlaneWidget.
177 177  
178 178  {{html}}
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179 179  <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>
180 180  {{/html}}
181 181  
208 +=== 4. Using siibra to retrieve connectivities from the EBRAINS KG ===
182 182  
183 -=== 3. Using siibra to retrieve connectivities from the EBRAINS KG ===
184 -
185 185  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.
186 186  
187 187  {{html}}
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188 188  <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>
189 189  {{/html}}
190 190  
216 +=== 5. Run a workflow as an HPB job ===
191 191  
192 -=== 4. Run a workflow as an HPB job ===
193 -
194 194  A workflow simulation which is run remotely, by submitting a job to an HPC site and getting back the results (TimeSeries object).
195 195  
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. 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).
223 +
224 +[[image:parallel-simulations.png||height="590" width="1100"]]
225 +
226 +
196 196  {{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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TVB Widgets