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  • vbi_workflow.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:
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156	156
157	157	[[image:timeseries-plotly.png||alt="view3.png" height="593" width="1100"]]
158	158
	159	+=== 3. Visualize posterior pairplot resulted from an inference workflow ===
	160	+
	161	+This functionality is available for the SamplePosterior component. Right click on the component and select the Open Viewer functionality.
	162	+
	163	+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.
	164	+
	165	+*Make sure the workflow has been executed so the viewer has data to load.
	166	+
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).
	175	+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
	181	+=== 2. Full VBI Inference workflow ===
173	173
174		-=== 2. Configuring model parameters using the PhasePlaneWidget: ===
	183	+Contains all VBI components required to run an inference workflow (e.g., inference configuration, model, simulator, train posterior, sample posterior).
175	175
	185	+[[image:vbi_workflow.png||height="590" width="1100"]]
	186	+
	187	+=== 3. Configuring model parameters using the PhasePlaneWidget: ===
	188	+
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
	195	+=== 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
	203	+=== 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
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}}

vbi_workflow.png

Author

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	1	+XWiki.teodoramisan

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	1	+465.2 KB

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