Last modified by paulapopa on 2023/03/24 08:17
From version 45.1
edited by paulapopa
on 2023/03/08 16:30
Change comment: There is no comment for this version
To version 54.1
edited by paulapopa
on 2023/03/08 17:06
Change comment: There is no comment for this version

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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 -== Jupyter Lab Extension for building and executing EBRAINS Workflows ==
5 +== Jupyter Lab Extension for building and executing TVB Workflows on EBRAINS ==
6 6  
7 7  == Purpose ==
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  
11 -**Note: **This extension is still a WIP (Work In Progress).
12 -
13 13  == Acknowledgements ==
14 14  
15 15  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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71 71  
72 72  === **Step 5. Run the workflow** ===
73 73  
74 -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.
72 +After connecting everything, you need to run the workflow to actually see its results.
75 75  
74 +There are 2 ways to run the workflow in EBRAINS Lab:
75 +
76 +~1. Locally:
77 +
78 +* 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.
79 +
76 76  [[image:run.png]]
77 77  
82 +
83 +2. Remotely on HPC (only if you have access to HPC resources)
84 +
85 +* First choose the __Remote Run__ in the select box and then click the Run button (▶), which will also implicitly compile the workflow.
86 +
87 +[[image:remote.png]]
88 +
89 +* A dialog will open to request the HPC connection details:
90 +** which __HPC Site__ to use
91 +** the name of the __HPC Project/Account__ you have access to
92 +** 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.
93 +** 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.
94 +
95 +[[image:rem.png]]
96 +
97 +* 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:
98 +
99 +[[image:uni.png]]
100 +
101 +
78 78  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.
79 79  
80 80  [[image:out.png]]
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84 84  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.
85 85  
86 86  
87 -
88 88  == Custom functionalities ==
89 89  
90 90  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.
91 91  
92 -=== 1. Configure TVB models using the Phase Plane widget. ===
115 +=== 1. Configure TVB models using the Phase Plane widget ===
93 93  
94 94  This functionality was added to make it easier for users to provide the correct parameters to TVB models, using the Phase Plane widget.
95 95  
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111 111  [[image:image-20221116130425-1.png||height="900" width="1069"]]
112 112  
113 113  
137 +=== 2. Visualize time series resulted from simulations ===
138 +
139 +
140 +[[image:view.png]]
141 +
142 +(% class="wikigeneratedid" %)
143 +=== ===
144 +
145 +[[image:view2.png]]
146 +
147 +
148 +
149 +[[image:view3.png]]
150 +
151 +(% class="wikigeneratedid" %)
152 +== ==
153 +
114 114  == Workflow examples ==
115 115  
116 116  (((
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TVB Widgets