Last modified by paulapopa on 2023/03/24 08:17
From version 52.1
edited by paulapopa
on 2023/03/08 17:06
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To version 57.1
edited by paulapopa
on 2023/03/24 08:10
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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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69 69  
70 70  === **Step 5. Run the workflow** ===
71 71  
72 -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.
73 73  
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 +
74 74  [[image:run.png]]
75 75  
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 +
76 76  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.
77 77  
78 78  [[image:out.png]]
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82 82  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.
83 83  
84 84  
85 -
86 86  == Custom functionalities ==
87 87  
88 88  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.
89 89  
90 -=== 1. Configure TVB models using the Phase Plane widget. ===
121 +=== 1. Configure TVB models using the Phase Plane widget ===
91 91  
92 92  This functionality was added to make it easier for users to provide the correct parameters to TVB models, using the Phase Plane widget.
93 93  
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109 109  [[image:image-20221116130425-1.png||height="900" width="1069"]]
110 110  
111 111  
143 +=== 2. Visualize time series resulted from simulations ===
144 +
145 +
146 +[[image:view.png]]
147 +
148 +=== ===
149 +
150 +[[image:view2.png]]
151 +
152 +
153 +
154 +[[image:view3.png]]
155 +
156 +== ==
157 +
112 112  == Workflow examples ==
113 113  
114 114  (((
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118 118  Contains all TVB components necessary for running a TVB simulation (i.e. connectivity, coupling, model, integrator, monitor, simulator).
119 119  
120 120  {{html}}
121 -<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>
122 122  {{/html}}
123 123  
124 124  
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127 127  Same workflow as before, but the parameter for the model used in simulation are set using the PhasePlaneWidget.
128 128  
129 129  {{html}}
130 -<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>
131 131  {{/html}}
132 132  
133 133  
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136 136  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.
137 137  
138 138  {{html}}
139 -<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>
140 140  {{/html}}
141 141  
142 142  
143 -=== 4. Run a workflow inside an HPB job ===
189 +=== 4. Run a workflow as an HPB job ===
144 144  
145 145  A workflow simulation which is run remotely, by submitting a job to an HPC site and getting back the results (TimeSeries object).
146 146  
147 -{{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}}
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