Attention: The EBRAINS drive will be unavailable for most of the weekend starting the 25th October. Although the Lab is availble while the Drive is down, files that are stored in the Drive will not be loaded and you will be unable to save documents directly on the Lab.


Last modified by paulapopa on 2023/03/24 08:17
From version 24.1
edited by rominabaila
on 2022/11/16 15:25
Change comment: Uploaded new attachment "image-20221116162514-1.png", version {1}
To version 34.1
edited by paulapopa
on 2023/03/08 15:36
Change comment: Uploaded new attachment "newxircs.png", version {1}

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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}}
90 90  
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Public

TVB Widgets