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  • 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. 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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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 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
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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 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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176	176
177	177	[[image:vbi_workflow.png||height="590" width="1100"]]
178	178
179		-(% class="wikigeneratedid" %)
180		-{{{ }}}
181		-
182		-
183	183	=== 3. Configuring model parameters using the PhasePlaneWidget: ===
184	184
185	185	Same workflow as before, but the parameter for the model used in simulation are set using the PhasePlaneWidget.
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188	188	<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>
189	189	{{/html}}
190	190
191		-
192	192	=== 4. Using siibra to retrieve connectivities from the EBRAINS KG ===
193	193
194	194	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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197	197	<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>
198	198	{{/html}}
199	199
200		-
201	201	=== 5. Run a workflow as an HPB job ===
202	202
203	203	A workflow simulation which is run remotely, by submitting a job to an HPC site and getting back the results (TimeSeries object).

plot-posteriors.png

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plot-timeseries-vbi.png

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