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  • newxircuits.png
  • side.png

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Author

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1		-XWiki.rominabaila
	1	+XWiki.paulapopa

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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	+
3	3	== Jupyter Lab Extension for building and executing EBRAINS Workflows ==
4	4
5	5	== Purpose ==
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24	24
25	25	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:
26	26
27		-[[image:image-20221116115659-2.png]]
	29	+[[image:side.png]]
28	28
	31	+
29	29	== **Usage** ==
30	30
31	31	=== **Step 1. Create a new Xircuits workflow** ===
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86	86
87	87	== Workflow examples ==
88	88
89		-{{html}}<iframe src="https://drive.google.com/file/d/1wZ1EWSPUAI2NgGzrQiUZHL-kLEydZ4RC/preview" width="840" height="480" allow="autoplay"></iframe>{{/html}}
	92	+(((
	93	+=== 1. Full TVB Simulation workflow ===
	94	+)))
	95	+
	96	+Contains all TVB components necessary for running a TVB simulation (i.e. connectivity, coupling, model, integrator, monitor, simulator).
	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}}
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