Last modified by teodoramisan on 2026/02/13 10:11
From version 59.1
edited by teodoramisan
on 2025/12/15 16:54
Change comment: There is no comment for this version
To version 65.4
edited by teodoramisan
on 2026/02/12 11:20
Change comment: There is no comment for this version

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4 4  
5 5  This extension is also installed already in EBRAINS lab, where it can be tested directly.
6 6  
7 -== Jupyter Lab Extension for building and executing TVB Workflows on EBRAINS ==
7 +== Jupyter Lab Extension for building and executing TVB and VBI Workflows on EBRAINS ==
8 8  
9 9  == Purpose ==
10 10  
11 -This is a Jupyter Lab extension that offers graphical support for TVB workflows. It is already available in the EBRAINS Lab and it allows users to configure and execute TVB simulations directly from a GUI, while drastically reducing the complexity of configuring them inside a Jupyter Lab notebook.
11 +This is a Jupyter Lab extension that offers graphical support for TVB and VBI workflows. It is already available in the EBRAINS Lab and it allows users to configure and execute TVB simulations and VBI inference workflows directly from a GUI, while drastically reducing the complexity of configuring them inside a Jupyter Lab notebook. Try edit
12 12  
13 13  {{html}}
14 14  <iframe width="1200" height="450" src="https://www.youtube.com/embed/-cjZOsU6PBg" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
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16 16  
17 17  == Acknowledgements ==
18 18  
19 -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.
19 +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, VBI and EBRAINS. These functionalities are detailed in a section below.
20 20  
21 21  == Installation ==
22 22  
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53 53  
54 54  Now, you can browse through the components, select the one you wish to use, then drag and drop it into the workflow area.
55 55  
56 +Customizable components can be identified by a suffix (e.g. **TVB_**SIMULATOR, **VBI_**SIMULATION_RUNNER).
57 +
56 56  [[image:xircuits-component-browser.png||alt="components.png"]]
57 57  
58 58  === **Step 3. Configure the components** ===
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59 59  
60 60  The components that are provided in this extensions are configurable, meaning you can set some parameters on almost every component. Some of the parameters are literals, while some parameters are results of other components.
61 61  
64 +Parameters marked with a star (*) are mandatory, the workflow will not run until all required parameters have values assigned.
65 +
62 62  In case of primitives you need to open the //General// tab from the components tray and drag the appropriate //literal//: float, int, string, dict, etc.
63 63  
64 64  The parameters need to be linked to the inputs of the component by dragging and dropping a connection from the output port of a literal/component towards the corresponding input port of the other component (e.g. the gray connections in the screenshot below).
65 65  
70 +Components and parameters include info buttons (i) that explain their purpose and how they are used (e.g. the simulator info panel below).
71 +
66 66  [[image:configure-components.png||alt="diagr.png"]]
67 67  
68 68  === **Step 4. Make connections** ===
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124 124  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:
125 125  
126 126  
127 -(% style="text-align:center" %)
128 -[[image:image-20221116125354-2.png||height="800" width="1130"]]
133 +[[image:open-viewer-on-models.png||alt="image-20221116125354-2.png" data-xwiki-image-style-alignment="center" height="800" width="1130"]]
129 129  
130 130  
131 131  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.
132 132  
133 -(% style="text-align:center" %)
134 -[[image:image-20221116125822-1.png||height="800" width="821"]]
138 +[[image:image-20221116125822-1.png||data-xwiki-image-style-alignment="center" height="800" width="821"]]
135 135  
136 136  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).
137 137  
138 -(% style="text-align:center" %)
139 -[[image:image-20221116130425-1.png||height="900" width="1069"]]
142 +[[image:export-model-configuration.png||alt="image-20221116130425-1.png" data-xwiki-image-style-alignment="center" height="900" width="1069"]]
140 140  
141 141  
142 142  === 2. Visualize time series resulted from simulations ===
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143 143  
144 144  This functionality is available for the **StoreResultsToDrive** component. Right click on the **StoreResultsToDrive** and select the **Open Viewer** option:
145 145  
146 -[[image:view.png]]
149 +[[image:open-viewer-button.png||alt="view.png"]]
147 147  
148 148  A new Jupyter tab should open, which contains a read-only Jupyter notebook. After running the cell, you should be able to see the **TimeSeriesBrowser **widget with the //**Collab**// and //**folder**// you have chosen for the **StoreResultsToDrive **component already loaded.
149 149  
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151 151  
152 152  Next, you should choose which time series file to display and click the **View time series button**.
153 153  
154 -[[image:view3.png]]
157 +[[image:timeseries-plotly.png||alt="view3.png"]]
155 155  
156 156  == ==
157 157  
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TVB Widgets