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  • parallel-simulations.png
  • plot-posteriors.png
  • plot-timeseries-vbi.png

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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
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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:
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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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197	197
198	198	[[image:vbi_workflow.png||height="590" width="1100"]]
199	199
	179	+(% class="wikigeneratedid" %)
	180	+{{{ }}}
	181	+
	182	+
200	200	=== 3. Configuring model parameters using the PhasePlaneWidget: ===
201	201
202	202	Same workflow as before, but the parameter for the model used in simulation are set using the PhasePlaneWidget.
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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}}
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	191	+
208	208	=== 4. Using siibra to retrieve connectivities from the EBRAINS KG ===
209	209
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.
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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}}
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	200	+
216	216	=== 5. Run a workflow as an HPB job ===
217	217
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}}
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parallel-simulations.png

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1		-XWiki.teodoramisan

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plot-posteriors.png

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plot-timeseries-vbi.png

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