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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 57.1
edited by paulapopa
on 2023/03/24 08:10
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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139 139  
140 140  [[image:view.png]]
141 141  
142 -(% class="wikigeneratedid" %)
143 -=== ===
148 +=== ===
144 144  
145 145  [[image:view2.png]]
146 146  
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148 148  
149 149  [[image:view3.png]]
150 150  
151 -(% class="wikigeneratedid" %)
152 -== ==
156 +== ==
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>
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>
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>
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>
173 173  {{/html}}
174 174  
175 175  
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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>
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>
182 182  {{/html}}
183 183  
184 184  
185 -=== 4. Run a workflow inside an HPB job ===
189 +=== 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}}
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}}
190 190  
Public

TVB Widgets