Last modified by paulapopa on 2023/03/24 08:17
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edited by paulapopa
on 2023/03/08 16:00
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edited by paulapopa
on 2023/03/24 08:10
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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 +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 ==
8 +
7 7  == Purpose ==
8 8  
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.
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.
10 10  
11 -**Note: **This extension is still a WIP (Work In Progress).
13 +{{html}}
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>
15 +{{/html}}
12 12  
13 -
14 14  == Acknowledgements ==
15 15  
16 16  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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17 17  
18 18  == Installation ==
19 19  
20 -The extension can installed using the official PyPi distribution ([[https:~~/~~/pypi.org/project/tvb-ext-xircuits/>>https://pypi.org/project/tvb-ext-xircuits/]]):
23 +The extension can be 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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28 28  
29 29  [[image:side.png]]
30 30  
31 -
32 32  == **Usage** ==
33 33  
34 34  === **Step 1. Create a new Xircuits workflow** ===
35 35  
36 -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.
38 +From the Jupyter Lab launcher, click on the **Xircuits File** icon, as in the screenshot below.
37 37  
40 +[[image:newxircs.png]]
41 +
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 +
44 +[[image:newfile.png]]
45 +
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 +
38 38  === **Step 2.  Drag components into the workflow area** ===
39 39  
40 -Open the components tray, browse through the components, select the one you wish to use and drag it into the workflow area.
50 +Open the components tray, from the left-side bar icon highlighted below.
41 41  
52 +[[image:tray.png]]
53 +
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 +
56 +[[image:components.png]]
57 +
42 42  === **Step 3. Configure the components** ===
43 43  
44 -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.
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.
45 45  
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 +
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 +
66 +[[image:diagr.png]]
67 +
46 46  === **Step 4. Make connections** ===
47 47  
48 -After dragging all your desired components in the workflow area, it's time to connect the components.
70 +After dragging all your desired components/literals in the workflow area, it's time to connect the components.
49 49  
50 -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.
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.
51 51  
74 +[[image:diagram.png]]
75 +
52 52  === **Step 5. Run the workflow** ===
53 53  
54 -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.
78 +After connecting everything, you need to run the workflow to actually see its results.
55 55  
80 +There are 2 ways to run the workflow in EBRAINS Lab:
81 +
82 +~1. Locally:
83 +
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 +
86 +[[image:run.png]]
87 +
88 +
89 +2. Remotely on HPC (only if you have access to HPC resources)
90 +
91 +* First choose the __Remote Run__ in the select box and then click the Run button (▶), which will also implicitly compile the workflow.
92 +
93 +[[image:remote.png]]
94 +
95 +* A dialog will open to request the HPC connection details:
96 +** which __HPC Site__ to use
97 +** the name of the __HPC Project/Account__ you have access to
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 +** 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 +
101 +[[image:rem.png]]
102 +
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:
104 +
105 +[[image:uni.png]]
106 +
107 +
56 56  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.
57 57  
110 +[[image:out.png]]
111 +
58 58  === **Step 6. Share your work*** ===
59 59  
60 60  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.
61 61  
62 62  
63 -
64 64  == Custom functionalities ==
65 65  
66 66  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.
67 67  
68 -=== 1. Configure TVB models using the Phase Plane widget. ===
121 +=== 1. Configure TVB models using the Phase Plane widget ===
69 69  
70 70  This functionality was added to make it easier for users to provide the correct parameters to TVB models, using the Phase Plane widget.
71 71  
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87 87  [[image:image-20221116130425-1.png||height="900" width="1069"]]
88 88  
89 89  
143 +=== 2. Visualize time series resulted from simulations ===
144 +
145 +
146 +[[image:view.png]]
147 +
148 +=== ===
149 +
150 +[[image:view2.png]]
151 +
152 +
153 +
154 +[[image:view3.png]]
155 +
156 +== ==
157 +
90 90  == Workflow examples ==
91 91  
92 92  (((
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96 96  Contains all TVB components necessary for running a TVB simulation (i.e. connectivity, coupling, model, integrator, monitor, simulator).
97 97  
98 98  {{html}}
99 -<iframe src="https://drive.google.com/file/d/14sVjWXmtfZB-Zt7i3MA26-MiNWwv3jZI/preview" width="1280" height="720" allow="autoplay"></iframe>
167 +<iframe width="1280" height="720" src="https://www.youtube.com/embed/bmqPlIJsWLk" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
100 100  {{/html}}
101 101  
102 102  
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105 105  Same workflow as before, but the parameter for the model used in simulation are set using the PhasePlaneWidget.
106 106  
107 107  {{html}}
108 -<iframe src="https://drive.google.com/file/d/1Puoi4-Ej4BhVwtdRzciPD_qNKMF0HvGT/preview" width="1280" height="720" allow="autoplay"></iframe>
176 +<iframe width="1280" height="720" src="https://www.youtube.com/embed/jhGfYul1z9k" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
109 109  {{/html}}
110 110  
111 111  
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114 114  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.
115 115  
116 116  {{html}}
117 -<iframe src="https://drive.google.com/file/d/1bakH6ZD96eMHnYSw1aasF_gNXt8sBS7D/preview" width="1280" height="720" allow="autoplay"></iframe>
185 +<iframe width="1280" height="720" src="https://www.youtube.com/embed/hnqTpFGCYMg" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
118 118  {{/html}}
119 119  
120 120  
121 -=== 4. Run a workflow inside an HPB job ===
189 +=== 4. Run a workflow as an HPB job ===
122 122  
123 123  A workflow simulation which is run remotely, by submitting a job to an HPC site and getting back the results (TimeSeries object).
124 124  
125 -{{html}}<iframe src="https://drive.google.com/file/d/1rvcj_9lGtR069iXlL3Rm1czMNdA3qmGM/preview" width="1280" height="720" allow="autoplay"></iframe>{{/html}}
193 +{{html}}<iframe width="1280" height="720" src="https://www.youtube.com/embed/M6rZClFgRrM" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>{{/html}}
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TVB Widgets