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Last modified by teodoramisan on 2025/12/15 16:59
From version 54.1
edited by paulapopa
on 2023/03/08 17:06
Change comment: There is no comment for this version
To version 59.1
edited by teodoramisan
on 2025/12/15 16:54
Change comment: There is no comment for this version

Summary

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1 -XWiki.paulapopa
1 +XWiki.teodoramisan
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2 2  
3 3  Release on Pypi: [[https:~~/~~/pypi.org/project/tvb-ext-xircuits/>>https://pypi.org/project/tvb-ext-xircuits/]]
4 4  
5 +This extension is also installed already in EBRAINS lab, where it can be tested directly.
6 +
5 5  == Jupyter Lab Extension for building and executing TVB Workflows on EBRAINS ==
6 6  
7 7  == Purpose ==
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8 8  
9 9  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.
10 10  
13 +{{html}}
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>
15 +{{/html}}
16 +
11 11  == Acknowledgements ==
12 12  
13 13  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.
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31 31  
32 32  From the Jupyter Lab launcher, click on the **Xircuits File** icon, as in the screenshot below.
33 33  
34 -[[image:newxircs.png]]
40 +[[image:xircuits-file-icon.png||alt="newxircs.png"]]
35 35  
36 36  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.
37 37  
38 -[[image:newfile.png]]
44 +[[image:xircuits-generated-file.png||alt="newfile.png"]]
39 39  
40 40  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.
41 41  
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43 43  
44 44  Open the components tray, from the left-side bar icon highlighted below.
45 45  
46 -[[image:tray.png]]
52 +[[image:xircuits-extension-icon.png||alt="tray.png"]]
47 47  
48 48  Now, you can browse through the components, select the one you wish to use, then drag and drop it into the workflow area.
49 49  
50 -[[image:components.png]]
56 +[[image:xircuits-component-browser.png||alt="components.png"]]
51 51  
52 52  === **Step 3. Configure the components** ===
53 53  
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57 57  
58 58  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).
59 59  
60 -[[image:diagr.png]]
66 +[[image:configure-components.png||alt="diagr.png"]]
61 61  
62 62  === **Step 4. Make connections** ===
63 63  
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65 65  
66 66  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.
67 67  
68 -[[image:diagram.png]]
74 +[[image:components-connection.png||alt="diagram.png"]]
69 69  
70 70  === **Step 5. Run the workflow** ===
71 71  
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77 77  
78 78  * 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.
79 79  
80 -[[image:run.png]]
86 +[[image:local-run-button.png||alt="run.png"]]
81 81  
82 82  
83 83  2. Remotely on HPC (only if you have access to HPC resources)
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84 84  
85 85  * First choose the __Remote Run__ in the select box and then click the Run button (▶), which will also implicitly compile the workflow.
86 86  
87 -[[image:remote.png]]
93 +[[image:remote-run-button.png||alt="remote.png"]]
88 88  
89 89  * A dialog will open to request the HPC connection details:
90 90  ** which __HPC Site__ to use
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92 92  ** 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.
93 93  ** 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.
94 94  
95 -[[image:rem.png]]
101 +[[image:remote-run-configuration.png||alt="rem.png"]]
96 96  
97 97  * 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:
98 98  
99 -[[image:uni.png]]
105 +[[image:hpc-monitoring.png||alt="uni.png"]]
100 100  
101 101  
102 102  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.
103 103  
104 -[[image:out.png]]
110 +[[image:jupyter-output-window.png||alt="out.png"]]
105 105  
106 106  === **Step 6. Share your work*** ===
107 107  
108 108  This step is, of course, optional, but it is worth mentioning that sharing your workflows with others is extremely easy. By just saving and sharing your workflow (*.xircuits) file, anyone can access the entire workflow, see the exact connections that you made and receive the same configuration for the components.
109 109  
110 -
111 111  == Custom functionalities ==
112 112  
113 113  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.
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136 136  
137 137  === 2. Visualize time series resulted from simulations ===
138 138  
144 +This functionality is available for the **StoreResultsToDrive** component. Right click on the **StoreResultsToDrive** and select the **Open Viewer** option:
139 139  
140 140  [[image:view.png]]
141 141  
142 -(% class="wikigeneratedid" %)
143 -=== ===
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.
144 144  
145 145  [[image:view2.png]]
146 146  
152 +Next, you should choose which time series file to display and click the **View time series button**.
147 147  
148 -
149 149  [[image:view3.png]]
150 150  
151 -(% class="wikigeneratedid" %)
152 -== ==
156 +== ==
153 153  
154 154  == Workflow examples ==
155 155  
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160 160  Contains all TVB components necessary for running a TVB simulation (i.e. connectivity, coupling, model, integrator, monitor, simulator).
161 161  
162 162  {{html}}
163 -<iframe src="https://drive.google.com/file/d/14sVjWXmtfZB-Zt7i3MA26-MiNWwv3jZI/preview" width="1280" height="720" allow="autoplay"></iframe>
167 +<iframe width="1280" height="720" src="https://www.youtube.com/embed/bmqPlIJsWLk" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
164 164  {{/html}}
165 165  
166 166  
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169 169  Same workflow as before, but the parameter for the model used in simulation are set using the PhasePlaneWidget.
170 170  
171 171  {{html}}
172 -<iframe src="https://drive.google.com/file/d/1Puoi4-Ej4BhVwtdRzciPD_qNKMF0HvGT/preview" width="1280" height="720" allow="autoplay"></iframe>
176 +<iframe width="1280" height="720" src="https://www.youtube.com/embed/jhGfYul1z9k" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
173 173  {{/html}}
174 174  
175 175  
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178 178  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.
179 179  
180 180  {{html}}
181 -<iframe src="https://drive.google.com/file/d/1bakH6ZD96eMHnYSw1aasF_gNXt8sBS7D/preview" width="1280" height="720" allow="autoplay"></iframe>
185 +<iframe width="1280" height="720" src="https://www.youtube.com/embed/hnqTpFGCYMg" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
182 182  {{/html}}
183 183  
184 184  
185 -=== 4. Run a workflow inside an HPB job ===
189 +=== 4. Run a workflow as an HPB job ===
186 186  
187 187  A workflow simulation which is run remotely, by submitting a job to an HPC site and getting back the results (TimeSeries object).
188 188  
189 -{{html}}<iframe src="https://drive.google.com/file/d/1rvcj_9lGtR069iXlL3Rm1czMNdA3qmGM/preview" width="1280" height="720" allow="autoplay"></iframe>{{/html}}
193 +{{html}}<iframe width="1280" height="720" src="https://www.youtube.com/embed/M6rZClFgRrM" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>{{/html}}
190 190  
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Public

TVB Widgets