Summary

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Author

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1		-XWiki.paulapopa
	1	+XWiki.ldomide

Content

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11	11	This is a Jupyter Lab extension that offers graphical support for TVB workflows. It is already available in the EBRAINS Lab and it allows users to configure and execute TVB simulations directly from a GUI, while drastically reducing the complexity of configuring them inside a Jupyter Lab notebook.
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13		-{{html}}
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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17	17	== Acknowledgements ==
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19	19	This extension is build on top of the [[Xircuits Jupyter extension>>https://xircuits.io/]], but it also comes with custom functionalities, specifically designed for TVB and EBRAINS. These functionalities are detailed in a section below.
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142	142
143	143	=== 2. Visualize time series resulted from simulations ===
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145		-This functionality is available for the **StoreResultsToDrive** component. Right click on the **StoreResultsToDrive** and select the **Open Viewer** option:
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147	147	[[image:view.png]]
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149		-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.
	144	+=== ===
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151	151	[[image:view2.png]]
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153		-Next, you should choose which time series file to display and click the **View time series button**.
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	149	+
155	155	[[image:view3.png]]
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157		-== ==
	152	+== ==
158	158
159	159	== Workflow examples ==
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165	165	Contains all TVB components necessary for running a TVB simulation (i.e. connectivity, coupling, model, integrator, monitor, simulator).
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167	167	{{html}}
168		-<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>
	163	+<iframe src="https://drive.google.com/file/d/14sVjWXmtfZB-Zt7i3MA26-MiNWwv3jZI/preview" width="1280" height="720" allow="autoplay"></iframe>
169	169	{{/html}}
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174	174	Same workflow as before, but the parameter for the model used in simulation are set using the PhasePlaneWidget.
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176	176	{{html}}
177		-<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>
	172	+<iframe src="https://drive.google.com/file/d/1Puoi4-Ej4BhVwtdRzciPD_qNKMF0HvGT/preview" width="1280" height="720" allow="autoplay"></iframe>
178	178	{{/html}}
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183	183	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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185	185	{{html}}
186		-<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>
	181	+<iframe src="https://drive.google.com/file/d/1bakH6ZD96eMHnYSw1aasF_gNXt8sBS7D/preview" width="1280" height="720" allow="autoplay"></iframe>
187	187	{{/html}}
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189	189
190		-=== 4. Run a workflow as an HPB job ===
	185	+=== 4. Run a workflow inside an HPB job ===
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192	192	A workflow simulation which is run remotely, by submitting a job to an HPC site and getting back the results (TimeSeries object).
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194		-{{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}}
	189	+{{html}}<iframe src="https://drive.google.com/file/d/1rvcj_9lGtR069iXlL3Rm1czMNdA3qmGM/preview" width="1280" height="720" allow="autoplay"></iframe>{{/html}}
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