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Author

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1		-XWiki.paulapopa
	1	+XWiki.rominabaila

Content

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1	1	Source code: [[https:~~/~~/github.com/the-virtual-brain/tvb-ext-xircuits>>https://github.com/the-virtual-brain/tvb-ext-xircuits]]
2	2
3		-Release on Pypi: [[https:~~/~~/pypi.org/project/tvb-ext-xircuits/>>https://pypi.org/project/tvb-ext-xircuits/]]
4		-
5	5	== Jupyter Lab Extension for building and executing EBRAINS Workflows ==
6	6
7	7	== Purpose ==
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26	26
27	27	After installing the extension and opening a Jupyter Lab session, you should be able to see in the left panel of Jupyter Lab a new icon, which represents the Xircuits components tray:
28	28
29		-[[image:side.png]]
	27	+[[image:image-20221116115659-2.png]]
30	30
31		-
32	32	== **Usage** ==
33	33
34	34	=== **Step 1. Create a new Xircuits workflow** ===
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89	89
90	90	== Workflow examples ==
91	91
92		-(((
93		-=== 1. Full TVB Simulation workflow ===
94		-)))
	89	+=== A TVB simulation workflow ===
95	95
96		-Contains all TVB components necessary for running a TVB simulation (i.e. connectivity, coupling, model, integrator, monitor, simulator).
	91	+(% style="text-align:center" %)
	92	+[[image:image-20221116162514-1.png||height="800" width="1456"]]
97	97
98		-{{html}}
99		-<iframe src="https://drive.google.com/file/d/14sVjWXmtfZB-Zt7i3MA26-MiNWwv3jZI/preview" width="1280" height="720" allow="autoplay"></iframe>
100		-{{/html}}
101		-
102		-
103		-=== 2. Configuring model parameters using the PhasePlaneWidget: ===
104		-
105		-Same workflow as before, but the parameter for the model used in simulation are set using the PhasePlaneWidget.
106		-
107		-{{html}}
108		-<iframe src="https://drive.google.com/file/d/1Puoi4-Ej4BhVwtdRzciPD_qNKMF0HvGT/preview" width="1280" height="720" allow="autoplay"></iframe>
109		-{{/html}}
110		-
111		-
112		-=== 3. Using siibra to retrieve connectivities from the EBRAINS KG ===
113		-
114		-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.
115		-
116		-{{html}}
117		-<iframe src="https://drive.google.com/file/d/1bakH6ZD96eMHnYSw1aasF_gNXt8sBS7D/preview" width="1280" height="720" allow="autoplay"></iframe>
118		-{{/html}}
119		-
120		-
121		-=== 4. Run a workflow inside an HPB job ===
122		-
123		-A workflow simulation which is run remotely, by submitting a job to an HPC site and getting back the results (TimeSeries object).
124		-
125		-{{html}}<iframe src="https://drive.google.com/file/d/1rvcj_9lGtR069iXlL3Rm1czMNdA3qmGM/preview" width="1280" height="720" allow="autoplay"></iframe>{{/html}}
	94	+{{html}}<iframe src="https://drive.google.com/file/d/1wZ1EWSPUAI2NgGzrQiUZHL-kLEydZ4RC/preview" width="840" height="480" allow="autoplay"></iframe>{{/html}}
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Author

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1		-XWiki.paulapopa

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1		-3.8 KB

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