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Author

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1		-XWiki.paulapopa
	1	+XWiki.teodoramisan

Content

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4	4
5	5	This extension is also installed already in EBRAINS lab, where it can be tested directly.
6	6
7		-== Jupyter Lab Extension for building and executing TVB Workflows on EBRAINS ==
	7	+== Jupyter Lab Extension for building and executing TVB and VBI Workflows on EBRAINS ==
8	8
9	9	== Purpose ==
10	10
11		-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. Try edit
	11	+This is a Jupyter Lab extension that offers graphical support for TVB and VBI workflows. It is already available in the EBRAINS Lab and it allows users to configure and execute TVB simulations and VBI inference workflows directly from a GUI, while drastically reducing the complexity of configuring them inside a Jupyter Lab notebook. Try edit
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13	13	{{html}}
14	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>
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16	16
17	17	== Acknowledgements ==
18	18
19		-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.
	19	+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, VBI and EBRAINS. These functionalities are detailed in a section below.
20	20
21	21	== Installation ==
22	22
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37	37
38	38	From the Jupyter Lab launcher, click on the **Xircuits File** icon, as in the screenshot below.
39	39
40		-[[image:xircuits-file-icon.png||alt="newxircs.png"]]
	40	+[[image:xircuits-file-icon.png||alt="newxircs.png" height="592" width="1100"]]
41	41
42	42	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.
43	43
44		-[[image:xircuits-generated-file.png||alt="newfile.png"]]
	44	+[[image:xircuits-generated-file.png||alt="newfile.png" height="592" width="1100"]]
45	45
46	46	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.
47	47
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49	49
50	50	Open the components tray, from the left-side bar icon highlighted below.
51	51
52		-[[image:xircuits-extension-icon.png||alt="tray.png"]]
	52	+[[image:xircuits-extension-icon.png||alt="tray.png" height="591" width="1100"]]
53	53
54	54	Now, you can browse through the components, select the one you wish to use, then drag and drop it into the workflow area.
55	55
56		-[[image:xircuits-component-browser.png||alt="components.png"]]
	56	+Customizable components can be identified by a suffix (e.g. **TVB_**SIMULATOR, **VBI_**SIMULATION_RUNNER).
57	57
	58	+[[image:xircuits-component-browser.png||alt="components.png" height="592" width="1100"]]
	59	+
58	58	=== **Step 3. Configure the components** ===
59	59
60	60	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.
61	61
	64	+Parameters marked with a star (*) are mandatory, the workflow will not run until all required parameters have values assigned.
	65	+
62	62	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.
63	63
64	64	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).
65	65
66		-[[image:configure-components.png||alt="diagr.png"]]
	70	+Components and parameters include info buttons (i) that explain their purpose and how they are used (e.g. the simulator info panel below).
67	67
	72	+[[image:Screenshot 2026-02-12 115445.png||alt="diagr.png" height="592" width="1100"]]
	73	+
68	68	=== **Step 4. Make connections** ===
69	69
70	70	After dragging all your desired components/literals in the workflow area, it's time to connect the components.
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71	71
72	72	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.
73	73
74		-[[image:components-connection.png||alt="diagram.png"]]
	80	+[[image:components-connection.png||alt="diagram.png" height="592" width="1100"]]
75	75
76	76	=== **Step 5. Run the workflow** ===
77	77
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83	83
84	84	* 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.
85	85
86		-[[image:local-run-button.png||alt="run.png"]]
	92	+[[image:local-run-button.png||alt="run.png" height="592" width="1100"]]
87	87
88	88
89	89	2. Remotely on HPC (only if you have access to HPC resources)
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90	90
91	91	* First choose the __Remote Run__ in the select box and then click the Run button (▶), which will also implicitly compile the workflow.
92	92
93		-[[image:remote-run-button.png||alt="remote.png"]]
	99	+[[image:remote-run-button.png||alt="remote.png" height="385" width="1100"]]
94	94
95	95	* A dialog will open to request the HPC connection details:
96	96	** which __HPC Site__ to use
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98	98	** 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.
99	99	** 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.
100	100
101		-[[image:remote-run-configuration.png||alt="rem.png"]]
	107	+[[image:remote-run-configuration.png||alt="rem.png" height="591" width="1100"]]
102	102
103	103	* 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:
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105		-[[image:hpc-monitoring.png||alt="uni.png"]]
	111	+[[image:hpc-monitoring.png||alt="uni.png" height="593" width="1100"]]
106	106
107	107
108	108	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.
109	109
110		-[[image:jupyter-output-window.png||alt="out.png"]]
	116	+[[image:jupyter-output-window.png||alt="out.png" height="591" width="1100"]]
111	111
112	112	=== **Step 6. Share your work*** ===
113	113

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	1	+XWiki.teodoramisan

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