Last modified by paulapopa on 2023/03/24 08:17
From version 58.1
edited by paulapopa
on 2023/03/24 08:17
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To version 49.1
edited by paulapopa
on 2023/03/08 16:49
Change comment: Uploaded new attachment "rem.png", version {1}

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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 -
7 7  == Jupyter Lab Extension for building and executing TVB Workflows on EBRAINS ==
8 8  
9 9  == Purpose ==
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10 10  
11 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.
12 12  
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 -
17 17  == Acknowledgements ==
18 18  
19 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.
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75 75  
76 76  === **Step 5. Run the workflow** ===
77 77  
78 -After connecting everything, you need to run the workflow to actually see its results.
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.
79 79  
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 -
86 86  [[image:run.png]]
87 87  
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 -
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  
110 110  [[image:out.png]]
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114 114  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.
115 115  
116 116  
85 +
117 117  == Custom functionalities ==
118 118  
119 119  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.
120 120  
121 -=== 1. Configure TVB models using the Phase Plane widget ===
90 +=== 1. Configure TVB models using the Phase Plane widget. ===
122 122  
123 123  This functionality was added to make it easier for users to provide the correct parameters to TVB models, using the Phase Plane widget.
124 124  
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140 140  [[image:image-20221116130425-1.png||height="900" width="1069"]]
141 141  
142 142  
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 -
159 159  == Workflow examples ==
160 160  
161 161  (((
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165 165  Contains all TVB components necessary for running a TVB simulation (i.e. connectivity, coupling, model, integrator, monitor, simulator).
166 166  
167 167  {{html}}
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>
121 +<iframe src="https://drive.google.com/file/d/14sVjWXmtfZB-Zt7i3MA26-MiNWwv3jZI/preview" width="1280" height="720" allow="autoplay"></iframe>
169 169  {{/html}}
170 170  
171 171  
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174 174  Same workflow as before, but the parameter for the model used in simulation are set using the PhasePlaneWidget.
175 175  
176 176  {{html}}
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>
130 +<iframe src="https://drive.google.com/file/d/1Puoi4-Ej4BhVwtdRzciPD_qNKMF0HvGT/preview" width="1280" height="720" allow="autoplay"></iframe>
178 178  {{/html}}
179 179  
180 180  
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183 183  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.
184 184  
185 185  {{html}}
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>
139 +<iframe src="https://drive.google.com/file/d/1bakH6ZD96eMHnYSw1aasF_gNXt8sBS7D/preview" width="1280" height="720" allow="autoplay"></iframe>
187 187  {{/html}}
188 188  
189 189  
190 -=== 4. Run a workflow as an HPB job ===
143 +=== 4. Run a workflow inside an HPB job ===
191 191  
192 192  A workflow simulation which is run remotely, by submitting a job to an HPC site and getting back the results (TimeSeries object).
193 193  
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}}
147 +{{html}}<iframe src="https://drive.google.com/file/d/1rvcj_9lGtR069iXlL3Rm1czMNdA3qmGM/preview" width="1280" height="720" allow="autoplay"></iframe>{{/html}}
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TVB Widgets