Last modified by paulapopa on 2023/03/24 08:17
From version 23.1
edited by rominabaila
on 2022/11/16 13:40
Change comment: There is no comment for this version
To version 33.1
edited by paulapopa
on 2023/03/08 15:34
Change comment: Uploaded new attachment "newxircx.png", version {1}

Summary

Details

Page properties
Author
... ... @@ -1,1 +1,1 @@
1 -XWiki.rominabaila
1 +XWiki.paulapopa
Content
... ... @@ -1,5 +1,7 @@
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 ==
... ... @@ -24,8 +24,9 @@
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** ===
... ... @@ -86,5 +86,38 @@
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  
image-20221116162514-1.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.rominabaila
Size
... ... @@ -1,0 +1,1 @@
1 +185.4 KB
Content
newxircuits.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.paulapopa
Size
... ... @@ -1,0 +1,1 @@
1 +406.6 KB
Content
newxircx.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.paulapopa
Size
... ... @@ -1,0 +1,1 @@
1 +392.9 KB
Content
side.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.paulapopa
Size
... ... @@ -1,0 +1,1 @@
1 +3.8 KB
Content
Public

TVB Widgets