Last modified by paulapopa on 2023/03/24 08:17
From version 33.1
edited by paulapopa
on 2023/03/08 15:34
Change comment: Uploaded new attachment "newxircx.png", version {1}
To version 25.3
edited by rominabaila
on 2022/11/25 15:57
Change comment: There is no comment for this version

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1 +XWiki.rominabaila
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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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96 96  Contains all TVB components necessary for running a TVB simulation (i.e. connectivity, coupling, model, integrator, monitor, simulator).
97 97  
98 98  {{html}}
99 -<iframe src="https://drive.google.com/file/d/14sVjWXmtfZB-Zt7i3MA26-MiNWwv3jZI/preview" width="1280" height="720" allow="autoplay"></iframe>
96 +<iframe src="https://drive.google.com/file/d/14sVjWXmtfZB-Zt7i3MA26-MiNWwv3jZI/preview" width="840" height="480" allow="autoplay"></iframe>
100 100  {{/html}}
101 101  
102 102  
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104 104  
105 105  Same workflow as before, but the parameter for the model used in simulation are set using the PhasePlaneWidget.
106 106  
107 -{{html}}
108 -<iframe src="https://drive.google.com/file/d/1Puoi4-Ej4BhVwtdRzciPD_qNKMF0HvGT/preview" width="1280" height="720" allow="autoplay"></iframe>
109 -{{/html}}
104 + {{html}}<iframe src="https://drive.google.com/file/d/1Puoi4-Ej4BhVwtdRzciPD_qNKMF0HvGT/preview" width="840" height="480" allow="autoplay"></iframe>{{/html}}
110 110  
111 111  
112 112  === 3. Using siibra to retrieve connectivities from the EBRAINS KG ===
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113 113  
114 114  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.
115 115  
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}}
126 -
111 + {{html}}<iframe src="https://drive.google.com/file/d/1bakH6ZD96eMHnYSw1aasF_gNXt8sBS7D/preview" width="840" height="480" allow="autoplay"></iframe>{{/html}}
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TVB Widgets