Last modified by paulapopa on 2023/03/24 08:17
From version 44.1
edited by paulapopa
on 2023/03/08 16:08
Change comment: There is no comment for this version
To version 25.3
edited by rominabaila
on 2022/11/25 15:57
Change comment: There is no comment for this version

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1 -XWiki.paulapopa
1 +XWiki.rominabaila
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1 1  Source code: [[https:~~/~~/github.com/the-virtual-brain/tvb-ext-xircuits>>https://github.com/the-virtual-brain/tvb-ext-xircuits]]
2 2  
3 -Release on Pypi: [[https:~~/~~/pypi.org/project/tvb-ext-xircuits/>>https://pypi.org/project/tvb-ext-xircuits/]]
4 -
5 5  == Jupyter Lab Extension for building and executing EBRAINS Workflows ==
6 6  
7 7  == Purpose ==
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17 17  
18 18  == Installation ==
19 19  
20 -The extension can be installed using the official PyPi distribution ([[https:~~/~~/pypi.org/project/tvb-ext-xircuits/>>https://pypi.org/project/tvb-ext-xircuits/]]):
18 +The extension can installed using the official PyPi distribution ([[https:~~/~~/pypi.org/project/tvb-ext-xircuits/>>https://pypi.org/project/tvb-ext-xircuits/]]):
21 21  
22 22  (% class="box" %)
23 23  (((
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26 26  
27 27  After installing the extension and opening a Jupyter Lab session, you should be able to see in the left panel of Jupyter Lab a new icon, which represents the Xircuits components tray:
28 28  
29 -[[image:side.png]]
27 +[[image:image-20221116115659-2.png]]
30 30  
31 31  == **Usage** ==
32 32  
33 33  === **Step 1. Create a new Xircuits workflow** ===
34 34  
35 -From the Jupyter Lab launcher, click on the **Xircuits File** icon, as in the screenshot below.
33 +Using the Jupyter Lab launcher. You will notice that 2 components are already placed inside the workflow: the Start and the Finish components. They cannot be modified or deleted, and they represent the starting and finishing point of the workflow.
36 36  
37 -[[image:newxircs.png]]
38 -
39 -A new file with the .xircuits extension will be generated under your current working directory. This is where you can start building the workflow diagram interactively.
40 -
41 -[[image:newfile.png]]
42 -
43 -You will notice that 2 components are already placed inside the workflow: the __Start__ and the __Finish__ components. They cannot be modified or deleted, and they represent the starting and finishing point of the workflow.
44 -
45 45  === **Step 2.  Drag components into the workflow area** ===
46 46  
47 -Open the components tray, from the left-side bar icon highlighted below.
37 +Open the components tray, browse through the components, select the one you wish to use and drag it into the workflow area.
48 48  
49 -[[image:tray.png]]
50 -
51 -Now, you can browse through the components, select the one you wish to use, then drag and drop it into the workflow area.
52 -
53 -[[image:components.png]]
54 -
55 55  === **Step 3. Configure the components** ===
56 56  
57 -The components that are provided in this extensions are configurable, meaning you can set some parameters on almost every component. Some of the parameters are literals, while some parameters are results of other components.
41 +The components that are provided in this extensions are configurable, meaning you can set some parameters on almost every component. For this  you need to open the //General// tab from the components tray and drag the appropriate //literal//: float, int, string, dict, etc.
58 58  
59 -In case of primitives you need to open the //General// tab from the components tray and drag the appropriate //literal//: float, int, string, dict, etc.
60 -
61 -The parameters need to be linked to the inputs of the component by dragging and dropping a connection from the output port of a literal/component towards the corresponding input port of the other component (e.g. the gray connections in the screenshot below).
62 -
63 -[[image:diagr.png]]
64 -
65 65  === **Step 4. Make connections** ===
66 66  
67 -After dragging all your desired components/literals in the workflow area, it's time to connect the components.
45 +After dragging all your desired components in the workflow area, it's time to connect the components.
68 68  
69 -First, link the __Start__ node to the first component of your workflow. Then make the connections between all your components. The last component should be linked to the __Finish__ node, to indicate the end of your workflow (e.g. the blue connections in the screenshot below). These connections will dictate the order of execution of the components in your workflow.
47 +First, link the Start node to the first component of your workflow. Then make the connections between all your components. The last component should be linked to the Finish node, to indicate the end of your workflow.
70 70  
71 -[[image:diagram.png]]
72 -
73 73  === **Step 5. Run the workflow** ===
74 74  
75 75  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.
76 76  
77 -[[image:run.png]]
78 -
79 79  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.
80 80  
81 -[[image:out.png]]
82 -
83 83  === **Step 6. Share your work*** ===
84 84  
85 85  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.
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121 121  Contains all TVB components necessary for running a TVB simulation (i.e. connectivity, coupling, model, integrator, monitor, simulator).
122 122  
123 123  {{html}}
124 -<iframe src="https://drive.google.com/file/d/14sVjWXmtfZB-Zt7i3MA26-MiNWwv3jZI/preview" width="1280" height="720" allow="autoplay"></iframe>
96 +<iframe src="https://drive.google.com/file/d/14sVjWXmtfZB-Zt7i3MA26-MiNWwv3jZI/preview" width="840" height="480" allow="autoplay"></iframe>
125 125  {{/html}}
126 126  
127 127  
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129 129  
130 130  Same workflow as before, but the parameter for the model used in simulation are set using the PhasePlaneWidget.
131 131  
132 -{{html}}
133 -<iframe src="https://drive.google.com/file/d/1Puoi4-Ej4BhVwtdRzciPD_qNKMF0HvGT/preview" width="1280" height="720" allow="autoplay"></iframe>
134 -{{/html}}
104 + {{html}}<iframe src="https://drive.google.com/file/d/1Puoi4-Ej4BhVwtdRzciPD_qNKMF0HvGT/preview" width="840" height="480" allow="autoplay"></iframe>{{/html}}
135 135  
136 136  
137 137  === 3. Using siibra to retrieve connectivities from the EBRAINS KG ===
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138 138  
139 139  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.
140 140  
141 -{{html}}
142 -<iframe src="https://drive.google.com/file/d/1bakH6ZD96eMHnYSw1aasF_gNXt8sBS7D/preview" width="1280" height="720" allow="autoplay"></iframe>
143 -{{/html}}
144 -
145 -
146 -=== 4. Run a workflow inside an HPB job ===
147 -
148 -A workflow simulation which is run remotely, by submitting a job to an HPC site and getting back the results (TimeSeries object).
149 -
150 -{{html}}<iframe src="https://drive.google.com/file/d/1rvcj_9lGtR069iXlL3Rm1czMNdA3qmGM/preview" width="1280" height="720" allow="autoplay"></iframe>{{/html}}
151 -
111 + {{html}}<iframe src="https://drive.google.com/file/d/1bakH6ZD96eMHnYSw1aasF_gNXt8sBS7D/preview" width="840" height="480" allow="autoplay"></iframe>{{/html}}
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TVB Widgets