Changes for page Extension tvb-ext-xircuits
Last modified by paulapopa on 2023/03/24 08:17
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... ... @@ -2,6 +2,8 @@ 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 == ... ... @@ -8,6 +8,10 @@ 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. ... ... @@ -136,20 +136,19 @@ 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 ... ... @@ -160,7 +160,7 @@ 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 ... ... @@ -169,7 +169,7 @@ 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 insidean 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