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 57.1
edited by paulapopa
on 2023/03/24 08:10
Change comment: There is no comment for this version
To version 55.1
edited by ldomide
on 2023/03/08 17:26
Change comment: There is no comment for this version

Summary

Details

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Author
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1 -XWiki.paulapopa
1 +XWiki.ldomide
Content
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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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145 145  
146 146  [[image:view.png]]
147 147  
148 -=== ===
144 +=== ===
149 149  
150 150  [[image:view2.png]]
151 151  
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153 153  
154 154  [[image:view3.png]]
155 155  
156 -== ==
152 +== ==
157 157  
158 158  == Workflow examples ==
159 159  
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164 164  Contains all TVB components necessary for running a TVB simulation (i.e. connectivity, coupling, model, integrator, monitor, simulator).
165 165  
166 166  {{html}}
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>
163 +<iframe src="https://drive.google.com/file/d/14sVjWXmtfZB-Zt7i3MA26-MiNWwv3jZI/preview" width="1280" height="720" allow="autoplay"></iframe>
168 168  {{/html}}
169 169  
170 170  
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173 173  Same workflow as before, but the parameter for the model used in simulation are set using the PhasePlaneWidget.
174 174  
175 175  {{html}}
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>
172 +<iframe src="https://drive.google.com/file/d/1Puoi4-Ej4BhVwtdRzciPD_qNKMF0HvGT/preview" width="1280" height="720" allow="autoplay"></iframe>
177 177  {{/html}}
178 178  
179 179  
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182 182  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.
183 183  
184 184  {{html}}
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>
181 +<iframe src="https://drive.google.com/file/d/1bakH6ZD96eMHnYSw1aasF_gNXt8sBS7D/preview" width="1280" height="720" allow="autoplay"></iframe>
186 186  {{/html}}
187 187  
188 188  
189 -=== 4. Run a workflow as an HPB job ===
185 +=== 4. Run a workflow inside an HPB job ===
190 190  
191 191  A workflow simulation which is run remotely, by submitting a job to an HPC site and getting back the results (TimeSeries object).
192 192  
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}}
189 +{{html}}<iframe src="https://drive.google.com/file/d/1rvcj_9lGtR069iXlL3Rm1czMNdA3qmGM/preview" width="1280" height="720" allow="autoplay"></iframe>{{/html}}
194 194  
Public

TVB Widgets