Last modified by teodoramisan on 2026/02/13 10:11
From version 77.2
edited by teodoramisan
on 2026/02/13 10:05
Change comment: There is no comment for this version
To version 73.2
edited by teodoramisan
on 2026/02/13 09:13
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  
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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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193 193  
194 194  === 2. Full VBI Inference workflow ===
195 195  
196 -Contains all VBI components required to run an inference workflow, from prior sampling and simulation to posterior training and posterior sampling.
175 +Contains all VBI components required to run an inference workflow (e.g., inference configuration, model, simulator, train posterior, sample posterior).
197 197  
198 -The workflow starts with **ConfigInference**, which builds the configuration inputs needed by the workflow. It samples parameter values from the prior distribution to generate theta and prepares the feature-extraction configuration (cfg) used later in the pipeline.
199 -
200 -
201 201  [[image:vbi_workflow.png||height="590" width="1100"]]
202 202  
203 203  === 3. Configuring model parameters using the PhasePlaneWidget: ===
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220 220  
221 221  A workflow simulation which is run remotely, by submitting a job to an HPC site and getting back the results (TimeSeries object).
222 222  
223 -=== 6. Parallel simulations workflow ===
224 -
225 -This example demonstrates **Parameter Space Exploration** (PSE) by running multiple TVB simulations in parallel for different parameter combinations.
226 -
227 -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).
228 -
229 -[[image:parallel-simulations.png||height="590" width="1100"]]
230 -
231 -
232 232  {{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}}
233 233  
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TVB Widgets