Last modified by teodoramisan on 2026/02/13 10:11
From version 62.1
edited by teodoramisan
on 2026/02/12 11:02
Change comment: There is no comment for this version
To version 67.1
edited by teodoramisan
on 2026/02/12 11:27
Change comment: There is no comment for this version

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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. Try edit
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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37 37  
38 38  From the Jupyter Lab launcher, click on the **Xircuits File** icon, as in the screenshot below.
39 39  
40 -[[image:xircuits-file-icon.png||alt="newxircs.png"]]
40 +[[image:xircuits-file-icon.png||alt="newxircs.png" height="592" width="1100"]]
41 41  
42 42  A new file with the .xircuits extension will be generated under your current working directory. This is where you can start building the workflow diagram interactively.
43 43  
44 -[[image:xircuits-generated-file.png||alt="newfile.png"]]
44 +[[image:xircuits-generated-file.png||alt="newfile.png" height="592" width="1100"]]
45 45  
46 46  You will notice that 2 components are already placed inside the workflow: the __Start__ and the __Finish__ components. They cannot be modified or deleted, and they represent the starting and finishing point of the workflow.
47 47  
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49 49  
50 50  Open the components tray, from the left-side bar icon highlighted below.
51 51  
52 -[[image:xircuits-extension-icon.png||alt="tray.png"]]
52 +[[image:xircuits-extension-icon.png||alt="tray.png" height="591" width="1100"]]
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 -[[image:xircuits-component-browser.png||alt="components.png"]]
56 +Customizable components can be identified by a suffix (e.g. **TVB_**SIMULATOR, **VBI_**SIMULATION_RUNNER).
57 57  
58 +[[image:xircuits-component-browser.png||alt="components.png" height="592" width="1100"]]
59 +
58 58  === **Step 3. Configure the components** ===
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  
66 -[[image:configure-components.png||alt="diagr.png"]]
70 +Components and parameters include info buttons (i) that explain their purpose and how they are used (e.g. the simulator info panel below).
67 67  
72 +[[image:Screenshot 2026-02-12 115445.png||alt="diagr.png" height="592" width="1100"]]
73 +
68 68  === **Step 4. Make connections** ===
69 69  
70 70  After dragging all your desired components/literals in the workflow area, it's time to connect the components.
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71 71  
72 72  First, link the __Start__ node to the first component of your workflow. Then make the connections between all your components. The last component should be linked to the __Finish__ node, to indicate the end of your workflow (e.g. the blue connections in the screenshot below). These connections will dictate the order of execution of the components in your workflow.
73 73  
74 -[[image:components-connection.png||alt="diagram.png"]]
80 +[[image:components-connection.png||alt="diagram.png" height="592" width="1100"]]
75 75  
76 76  === **Step 5. Run the workflow** ===
77 77  
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83 83  
84 84  * For this you can click on the Run button (▶), which will also implicitly compile the workflow. Make sure that __Local Run__ is selected near the Run button.
85 85  
86 -[[image:local-run-button.png||alt="run.png"]]
92 +[[image:local-run-button.png||alt="run.png" height="592" width="1100"]]
87 87  
88 88  
89 89  2. Remotely on HPC (only if you have access to HPC resources)
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90 90  
91 91  * First choose the __Remote Run__ in the select box and then click the Run button (▶), which will also implicitly compile the workflow.
92 92  
93 -[[image:remote-run-button.png||alt="remote.png"]]
99 +[[image:remote-run-button.png||alt="remote.png" height="385" width="1100"]]
94 94  
95 95  * A dialog will open to request the HPC connection details:
96 96  ** which __HPC Site__ to use
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98 98  ** one checkbox to choose whether you want the __HPC Monitoring__ to be opened up automatically (via tvb-ext-unicore GUI). This can also be opened up manually using the __Monitor HPC__ button or the __U__ icon from the left side-bar.
99 99  ** one checkbox to choose whether you want the results to be __staged out__ automatically or not. If checked, the workflow waits for the HPC jobs to finish and then performs the stage out. If unchecked, the results can be manually downloaded later on by using the GUI of the tvb-ext-unicore.
100 100  
101 -[[image:remote-run-configuration.png||alt="rem.png"]]
107 +[[image:remote-run-configuration.png||alt="rem.png" height="591" width="1100"]]
102 102  
103 103  * The HPC monitoring is done via the GUI of tvb-ext-unicore which is a separate package we have documented under this Wiki. But it can be nicely used together with tvb-ext-xircuits:
104 104  
105 -[[image:hpc-monitoring.png||alt="uni.png"]]
111 +[[image:hpc-monitoring.png||alt="uni.png" height="593" width="1100"]]
106 106  
107 107  
108 108  After clicking on Run, a new Jupyter Output window should appear in the bottom of your Jupyter Lab environment. Here you will see the output of your workflow, such as logs, static plots, etc.
109 109  
110 -[[image:jupyter-output-window.png||alt="out.png"]]
116 +[[image:jupyter-output-window.png||alt="out.png" height="591" width="1100"]]
111 111  
112 112  === **Step 6. Share your work*** ===
113 113  
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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 -[[image:open-viewer-on-models.png||alt="image-20221116125354-2.png" data-xwiki-image-style-alignment="center" height="800" width="1130"]]
133 +[[image:open-viewer-on-models.png||alt="image-20221116125354-2.png" data-xwiki-image-style-alignment="center" height="593" width="1100"]]
128 128  
129 129  
130 130  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.
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133 133  
134 134  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).
135 135  
136 -[[image:export-model-configuration.png||alt="image-20221116130425-1.png" data-xwiki-image-style-alignment="center" height="900" width="1069"]]
142 +[[image:export-model-configuration.png||alt="image-20221116130425-1.png" data-xwiki-image-style-alignment="center" height="763" width="1000"]]
137 137  
138 138  
139 139  === 2. Visualize time series resulted from simulations ===
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140 140  
141 141  This functionality is available for the **StoreResultsToDrive** component. Right click on the **StoreResultsToDrive** and select the **Open Viewer** option:
142 142  
143 -[[image:open-viewer-button.png||alt="view.png"]]
149 +[[image:open-viewer-button.png||alt="view.png" height="591" width="1100"]]
144 144  
145 145  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.
146 146  
147 -[[image:view2.png]]
153 +[[image:view2.png||height="576" width="1100"]]
148 148  
149 149  Next, you should choose which time series file to display and click the **View time series button**.
150 150  
151 -[[image:timeseries-plotly.png||alt="view3.png"]]
157 +[[image:timeseries-plotly.png||alt="view3.png" height="593" width="1100"]]
152 152  
153 153  == ==
154 154  
Screenshot 2026-02-12 115445.png
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TVB Widgets