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TVB logo VBT logo

tvb-ext-xircuits

This is a jupyterlab extension built as a prototype for building EBRAINS (including TVB simulator, Siibra API) workflows in a visual and interactive manner. It extends the already existent Xircuits jupyterlab extension by adding new components and new features on top.

Starting with version 2.0.0, tvb-ext-xircuits can be installed in lightweight mode or in full mode.

Full mode means that the extension will be fully working and able to run workflows.

Lightweight mode means that only the front-end part of the extension will be available, meaning that the users will be able to see all the extension's components, but running workflows will not work.

To install the extension locally and in full mode (recommended):

pip install tvb-ext-xircuits[full]

To install the extension in lightweight mode (only for specialized users):

pip install tvb-ext-xircuits

For dev mode setup there are 2 alternatives:

  1. Using jlpm:

    jlpm is a JupyterLab-provided, locked version of yarn and has a similar usage:

    conda activate [my-env]
pip install --upgrade pip
pip install -e .[full]
jupyter labextension develop . --overwrite  # Link your development version of the extension with JupyterLab
jupyter server extension enable tvbextxircuits  # Enable the server extension
tvbextxircuits

  2. Using yarn:

    You need to have a dedicated Python env, yarn, rust and cargo (from https://rustup.rs/) prepared:

    conda activate [my-env]
pip install --upgrade pip
pip install -e .[full]
yarn install
yarn install:extension
tvbextxircuits

To rebuild the extension after making changes to it:

  # Rebuild Typescript source after making changes
  jlpm build
  # Rebuild extension after making any changes
  jupyter lab build

To rebuild automatically:

  # Watch the source directory in another terminal tab
  jlpm run watch
  # Run Xircuits in watch mode in one terminal tab
  jupyter lab --watch

Notes

To be able to see details info related to TVB components you must first run the command python generate_description_files.py

Notebooks generated can be found at TVB_generated_notebooks/<xircuits_id>

Acknowledgments

Copyright (c) 2022-2024 to Xircuits Team See: https://github.com/XpressAI/xircuits

Copyright (c) 2022-2023 to TVB-Xircuits team (SDL Neuroscience Juelich, INS Marseille, Codemart) for changes in this fork.

Copyright (c) 2024 to Codemart - Brainiacs team for further changes in this fork.

This extension is build on top of the Xircuits https://xircuits.io Jupyter extension, and it adds custom features, tailored for EBRAINS env.

This project has received funding from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Specific Grant Agreement No. 945539 (Human Brain Project SGA3).

This project has received funding from the European Union’s Horizon Europe Programme under the Specific Grant Agreement No. 101147319 (EBRAINS 2.0 Project).

This project has received funding from the European Union’s Research and Innovation Program Horizon Europe under Grant Agreement No. 101137289 (Virtual Brain Twin Project).