Last modified by paulapopa on 2023/03/24 08:17
From version 55.1
edited by ldomide
on 2023/03/08 17:26
Change comment: There is no comment for this version
To version 51.1
edited by paulapopa
on 2023/03/08 17:03
Change comment: Uploaded new attachment "view.png", version {1}

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1 +XWiki.paulapopa
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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 -
7 7  == Jupyter Lab Extension for building and executing TVB Workflows on EBRAINS ==
8 8  
9 9  == Purpose ==
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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 results.
72 +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.
75 75  
76 -There are 2 ways to run the workflow in EBRAINS Lab:
77 -
78 -~1. Locally:
79 -
80 -* 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.
81 -
82 82  [[image:run.png]]
83 83  
84 -
85 -2. Remotely on HPC (only if you have access to HPC resources)
86 -
87 -* First choose the __Remote Run__ in the select box and then click the Run button (▶), which will also implicitly compile the workflow.
88 -
89 -[[image:remote.png]]
90 -
91 -* A dialog will open to request the HPC connection details:
92 -** which __HPC Site__ to use
93 -** the name of the __HPC Project/Account__ you have access to
94 -** 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.
95 -** 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.
96 -
97 -[[image:rem.png]]
98 -
99 -* 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:
100 -
101 -[[image:uni.png]]
102 -
103 -
104 104  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.
105 105  
106 106  [[image:out.png]]
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110 110  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.
111 111  
112 112  
85 +
113 113  == Custom functionalities ==
114 114  
115 115  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.
116 116  
117 -=== 1. Configure TVB models using the Phase Plane widget ===
90 +=== 1. Configure TVB models using the Phase Plane widget. ===
118 118  
119 119  This functionality was added to make it easier for users to provide the correct parameters to TVB models, using the Phase Plane widget.
120 120  
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136 136  [[image:image-20221116130425-1.png||height="900" width="1069"]]
137 137  
138 138  
139 -=== 2. Visualize time series resulted from simulations ===
140 -
141 -
142 -[[image:view.png]]
143 -
144 -=== ===
145 -
146 -[[image:view2.png]]
147 -
148 -
149 -
150 -[[image:view3.png]]
151 -
152 -== ==
153 -
154 154  == Workflow examples ==
155 155  
156 156  (((
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TVB Widgets