Last modified by paulapopa on 2023/03/24 08:17
From version 43.1
edited by paulapopa
on 2023/03/08 16:01
Change comment: There is no comment for this version
To version 58.1
edited by paulapopa
on 2023/03/24 08:17
Change comment: There is no comment for this version

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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 -== Jupyter Lab Extension for building and executing EBRAINS Workflows ==
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 ==
8 +
7 7  == Purpose ==
8 8  
9 -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.
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.
10 10  
11 -**Note: **This extension is still a WIP (Work In Progress).
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}}
12 12  
13 -
14 14  == Acknowledgements ==
15 15  
16 16  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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17 17  
18 18  == Installation ==
19 19  
20 -The extension can installed using the official PyPi distribution ([[https:~~/~~/pypi.org/project/tvb-ext-xircuits/>>https://pypi.org/project/tvb-ext-xircuits/]]):
23 +The extension can be installed using the official PyPi distribution ([[https:~~/~~/pypi.org/project/tvb-ext-xircuits/>>https://pypi.org/project/tvb-ext-xircuits/]]):
21 21  
22 22  (% class="box" %)
23 23  (((
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28 28  
29 29  [[image:side.png]]
30 30  
31 -
32 32  == **Usage** ==
33 33  
34 34  === **Step 1. Create a new Xircuits workflow** ===
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73 73  
74 74  === **Step 5. Run the workflow** ===
75 75  
76 -After connecting everything, you need to run the workflow to actually see its result. For this you can click on the Run button (▶), which will also implicitly compile the workflow.
78 +After connecting everything, you need to run the workflow to actually see its results.
77 77  
80 +There are 2 ways to run the workflow in EBRAINS Lab:
81 +
82 +~1. Locally:
83 +
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 +
78 78  [[image:run.png]]
79 79  
88 +
89 +2. Remotely on HPC (only if you have access to HPC resources)
90 +
91 +* First choose the __Remote Run__ in the select box and then click the Run button (▶), which will also implicitly compile the workflow.
92 +
93 +[[image:remote.png]]
94 +
95 +* A dialog will open to request the HPC connection details:
96 +** which __HPC Site__ to use
97 +** the name of the __HPC Project/Account__ you have access to
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 +** 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 +
101 +[[image:rem.png]]
102 +
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 +
105 +[[image:uni.png]]
106 +
107 +
80 80  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.
81 81  
82 82  [[image:out.png]]
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86 86  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.
87 87  
88 88  
89 -
90 90  == Custom functionalities ==
91 91  
92 92  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.
93 93  
94 -=== 1. Configure TVB models using the Phase Plane widget. ===
121 +=== 1. Configure TVB models using the Phase Plane widget ===
95 95  
96 96  This functionality was added to make it easier for users to provide the correct parameters to TVB models, using the Phase Plane widget.
97 97  
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113 113  [[image:image-20221116130425-1.png||height="900" width="1069"]]
114 114  
115 115  
143 +=== 2. Visualize time series resulted from simulations ===
144 +
145 +This functionality is available for the **StoreResultsToDrive** component. Right click on the **StoreResultsToDrive** and select the **Open Viewer** option:
146 +
147 +[[image:view.png]]
148 +
149 +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.
150 +
151 +[[image:view2.png]]
152 +
153 +Next, you should choose which time series file to display and click the **View time series button**.
154 +
155 +[[image:view3.png]]
156 +
157 +== ==
158 +
116 116  == Workflow examples ==
117 117  
118 118  (((
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122 122  Contains all TVB components necessary for running a TVB simulation (i.e. connectivity, coupling, model, integrator, monitor, simulator).
123 123  
124 124  {{html}}
125 -<iframe src="https://drive.google.com/file/d/14sVjWXmtfZB-Zt7i3MA26-MiNWwv3jZI/preview" width="1280" height="720" allow="autoplay"></iframe>
168 +<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>
126 126  {{/html}}
127 127  
128 128  
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131 131  Same workflow as before, but the parameter for the model used in simulation are set using the PhasePlaneWidget.
132 132  
133 133  {{html}}
134 -<iframe src="https://drive.google.com/file/d/1Puoi4-Ej4BhVwtdRzciPD_qNKMF0HvGT/preview" width="1280" height="720" allow="autoplay"></iframe>
177 +<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>
135 135  {{/html}}
136 136  
137 137  
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140 140  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.
141 141  
142 142  {{html}}
143 -<iframe src="https://drive.google.com/file/d/1bakH6ZD96eMHnYSw1aasF_gNXt8sBS7D/preview" width="1280" height="720" allow="autoplay"></iframe>
186 +<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>
144 144  {{/html}}
145 145  
146 146  
147 -=== 4. Run a workflow inside an HPB job ===
190 +=== 4. Run a workflow as an HPB job ===
148 148  
149 149  A workflow simulation which is run remotely, by submitting a job to an HPC site and getting back the results (TimeSeries object).
150 150  
151 -{{html}}<iframe src="https://drive.google.com/file/d/1rvcj_9lGtR069iXlL3Rm1czMNdA3qmGM/preview" width="1280" height="720" allow="autoplay"></iframe>{{/html}}
194 +{{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}}
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TVB Widgets