Last modified by paulapopa on 2023/03/24 08:17
From version 44.1
edited by paulapopa
on 2023/03/08 16:08
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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72 72  
73 73  === **Step 5. Run the workflow** ===
74 74  
75 -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.
76 76  
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 +
77 77  [[image:run.png]]
78 78  
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 +
79 79  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.
80 80  
81 81  [[image:out.png]]
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85 85  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.
86 86  
87 87  
88 -
89 89  == Custom functionalities ==
90 90  
91 91  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.
92 92  
93 -=== 1. Configure TVB models using the Phase Plane widget. ===
121 +=== 1. Configure TVB models using the Phase Plane widget ===
94 94  
95 95  This functionality was added to make it easier for users to provide the correct parameters to TVB models, using the Phase Plane widget.
96 96  
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112 112  [[image:image-20221116130425-1.png||height="900" width="1069"]]
113 113  
114 114  
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 +
115 115  == Workflow examples ==
116 116  
117 117  (((
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121 121  Contains all TVB components necessary for running a TVB simulation (i.e. connectivity, coupling, model, integrator, monitor, simulator).
122 122  
123 123  {{html}}
124 -<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>
125 125  {{/html}}
126 126  
127 127  
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130 130  Same workflow as before, but the parameter for the model used in simulation are set using the PhasePlaneWidget.
131 131  
132 132  {{html}}
133 -<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>
134 134  {{/html}}
135 135  
136 136  
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139 139  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.
140 140  
141 141  {{html}}
142 -<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>
143 143  {{/html}}
144 144  
145 145  
146 -=== 4. Run a workflow inside an HPB job ===
190 +=== 4. Run a workflow as an HPB job ===
147 147  
148 148  A workflow simulation which is run remotely, by submitting a job to an HPC site and getting back the results (TimeSeries object).
149 149  
150 -{{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