Attention: The EBRAINS drive will be unavailable for most of the weekend starting the 25th October. Although the Lab is availble while the Drive is down, files that are stored in the Drive will not be loaded and you will be unable to save documents directly on the Lab.


Last modified by paulapopa on 2023/03/24 08:17
From version 54.1
edited by paulapopa
on 2023/03/08 17:06
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

Summary

Details

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Content
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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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136 136  
137 137  === 2. Visualize time series resulted from simulations ===
138 138  
145 +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 -=== ===
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.
144 144  
145 145  [[image:view2.png]]
146 146  
153 +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 -== ==
157 +== ==
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>
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>
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>
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>
173 173  {{/html}}
174 174  
175 175  
... ... @@ -178,13 +178,13 @@
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>
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>
182 182  {{/html}}
183 183  
184 184  
185 -=== 4. Run a workflow inside an HPB job ===
190 +=== 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}}
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}}
190 190  
Public

TVB Widgets