Last modified by paulapopa on 2023/03/24 08:17
From version 13.1
edited by rominabaila
on 2022/11/16 11:38
Change comment: There is no comment for this version
To version 25.2
edited by rominabaila
on 2022/11/25 15:54
Change comment: There is no comment for this version

Summary

Details

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4 4  
5 5  == Purpose ==
6 6  
7 -This is a Jupyter Lab extension with the role of offering graphical support for EBRAINS workflows. It allows users to utilize all the TVB and EBRAINS capabilities, while drastically reducing the complexity of configuring them inside a Jupyter Lab environmen.
7 +This is a Jupyter Lab extension with the role of offering graphical support for EBRAINS workflows. It allows users to utilize all the TVB and EBRAINS capabilities, while drastically reducing the complexity of configuring them inside a Jupyter Lab environment.
8 8  
9 9  **Note: **This extension is still a WIP (Work In Progress).
10 10  
11 +
12 +== Acknowledgements ==
13 +
14 +This extension is build on top of the [[Xircuits Jupyter extension>>https://xircuits.io/]], but it also comes with custom functionalities, specifically designed for TVB and EBRAINS. These functionalities are detailed in a section below.
15 +
11 11  == Installation ==
12 12  
13 13  The extension can installed using the official PyPi distribution ([[https:~~/~~/pypi.org/project/tvb-ext-xircuits/>>https://pypi.org/project/tvb-ext-xircuits/]]):
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53 53  
54 54  
55 55  
61 +== Custom functionalities ==
56 56  
57 -
63 +As mentioned before, besides all the core functionalities provided by Xircuits, some other functionalities were added to better suit the needs of the EBRAINS users.
64 +
65 +=== 1. Configure TVB models using the Phase Plane widget. ===
66 +
67 +This functionality was added to make it easier for users to provide the correct parameters to TVB models, using the Phase Plane widget.
68 +
69 +To use this functionality, drag any model from the **TVB_MODELS** (inside the components tray) into the workflow area. Then right click on the model and select the **Open Viewer** option:
70 +
71 +
72 +(% style="text-align:center" %)
73 +[[image:image-20221116125354-2.png||height="800" width="1130"]]
74 +
75 +
76 +A new Jupyter tab should open, which contains a read-only Jupyter notebook. After following the instructions provided there, you should be able to see the Phase Plane widget associated with this particular model.
77 +
78 +(% style="text-align:center" %)
79 +[[image:image-20221116125822-1.png||height="800" width="821"]]
80 +
81 +After configuring the parameters with the desired values, go to the Exports tab of the widget and click on **Export model configuration**. Now all you have to do is to go back to the tab where your workflow is and you will see that the model will have values set for all the parameters that you modified in the Phase Plane widget (that is all the parameters there were assigned values different than the default ones).
82 +
83 +(% style="text-align:center" %)
84 +[[image:image-20221116130425-1.png||height="900" width="1069"]]
85 +
86 +
87 +== Workflow examples ==
88 +
89 +(((
90 +=== 1. Full TVB Simulation workflow ===
91 +)))
92 +
93 +Contains all TVB components necessary for running a TVB simulation (i.e. connectivity, coupling, model, integrator, monitor, simulator).
94 +
95 +{{html}}
96 +<iframe src="https://drive.google.com/file/d/14sVjWXmtfZB-Zt7i3MA26-MiNWwv3jZI/preview" width="840" height="480" allow="autoplay"></iframe>
97 +{{/html}}
98 +
99 +
100 +=== 2. Configuring model parameters using the PhasePlaneWidget: ===
101 +
102 +Same workflow as before, but the parameter for the model used in simulation are set using the PhasePlaneWidget.
103 +
104 + {{html}}<iframe src="https://drive.google.com/file/d/1Puoi4-Ej4BhVwtdRzciPD_qNKMF0HvGT/preview" width="840" height="480" allow="autoplay"></iframe>{{/html}}
2022-11-16 14-05-53.mp4
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Public

TVB Widgets