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 43.1
edited by paulapopa
on 2023/03/08 16:01
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 TVB Workflows on EBRAINS ==
5 +== Jupyter Lab Extension for building and executing EBRAINS Workflows ==
6 6  
7 7  == Purpose ==
8 8  
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.
9 +This is a Jupyter Lab extension with the role of offering graphical support for EBRAINS workflows. It allows users to utilize all the TVB and EBRAINS capabilities, while drastically reducing the complexity of configuring them inside a Jupyter Lab environment.
10 10  
11 +**Note: **This extension is still a WIP (Work In Progress).
12 +
13 +
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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14 14  
15 15  == Installation ==
16 16  
17 -The extension can be installed using the official PyPi distribution ([[https:~~/~~/pypi.org/project/tvb-ext-xircuits/>>https://pypi.org/project/tvb-ext-xircuits/]]):
20 +The extension can installed using the official PyPi distribution ([[https:~~/~~/pypi.org/project/tvb-ext-xircuits/>>https://pypi.org/project/tvb-ext-xircuits/]]):
18 18  
19 19  (% class="box" %)
20 20  (((
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25 25  
26 26  [[image:side.png]]
27 27  
31 +
28 28  == **Usage** ==
29 29  
30 30  === **Step 1. Create a new Xircuits workflow** ===
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69 69  
70 70  === **Step 5. Run the workflow** ===
71 71  
72 -After connecting everything, you need to run the workflow to actually see its results.
76 +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.
73 73  
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 -
80 80  [[image:run.png]]
81 81  
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 -
102 102  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.
103 103  
104 104  [[image:out.png]]
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108 108  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.
109 109  
110 110  
89 +
111 111  == Custom functionalities ==
112 112  
113 113  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.
114 114  
115 -=== 1. Configure TVB models using the Phase Plane widget ===
94 +=== 1. Configure TVB models using the Phase Plane widget. ===
116 116  
117 117  This functionality was added to make it easier for users to provide the correct parameters to TVB models, using the Phase Plane widget.
118 118  
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134 134  [[image:image-20221116130425-1.png||height="900" width="1069"]]
135 135  
136 136  
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 -
154 154  == Workflow examples ==
155 155  
156 156  (((
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Public

TVB Widgets