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 33.1
edited by paulapopa
on 2023/03/08 15:34
Change comment: Uploaded new attachment "newxircx.png", version {1}
To version 26.1
edited by rominabaila
on 2022/11/25 16:03
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="1920" height="1080" allow="autoplay"></iframe>
100 100  {{/html}}
101 101  
102 102  
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105 105  Same workflow as before, but the parameter for the model used in simulation are set using the PhasePlaneWidget.
106 106  
107 107  {{html}}
108 -<iframe src="https://drive.google.com/file/d/1Puoi4-Ej4BhVwtdRzciPD_qNKMF0HvGT/preview" width="1280" height="720" allow="autoplay"></iframe>
105 +<iframe src="https://drive.google.com/file/d/1Puoi4-Ej4BhVwtdRzciPD_qNKMF0HvGT/preview" width="1920" height="1080" allow="autoplay"></iframe>
109 109  {{/html}}
110 110  
111 111  
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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  
116 116  {{html}}
117 -<iframe src="https://drive.google.com/file/d/1bakH6ZD96eMHnYSw1aasF_gNXt8sBS7D/preview" width="1280" height="720" allow="autoplay"></iframe>
114 +<iframe src="https://drive.google.com/file/d/1bakH6ZD96eMHnYSw1aasF_gNXt8sBS7D/preview" width="1920" height="1080" allow="autoplay"></iframe>
118 118  {{/html}}
119 119  
120 120  
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122 122  
123 123  A workflow simulation which is run remotely, by submitting a job to an HPC site and getting back the results (TimeSeries object).
124 124  
125 -{{html}}<iframe src="https://drive.google.com/file/d/1rvcj_9lGtR069iXlL3Rm1czMNdA3qmGM/preview" width="1280" height="720" allow="autoplay"></iframe>{{/html}}
122 +{{html}}<iframe src="https://drive.google.com/file/d/1rvcj_9lGtR069iXlL3Rm1czMNdA3qmGM/preview" width="1920" height="1080" allow="autoplay"></iframe>{{/html}}
126 126  
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Public

TVB Widgets