Last modified by paulapopa on 2023/03/24 08:17
From version 34.1
edited by paulapopa
on 2023/03/08 15:36
Change comment: Uploaded new attachment "newxircs.png", version {1}
To version 25.1
edited by rominabaila
on 2022/11/16 15:25
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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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}}
126 126  
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Public

TVB Widgets