The Virtual Brain & Xircuits: a success story in neuroscience
A simulation in The Virtual Brain created with Xircuits
Codemart is celebrating this success story by being part of XpressAI’s cool 2024 Advent Calendar 🎄
The Virtual Brain (TVB) is one of the most beloved projects at Codemart. They've been proudly growing it for over 12 years, with the goal of helping the neuroscience community understand how the most complex organ in the human body works.
Over the years Codemart has collaborated with countless talented brain enthusiasts, from all over the world: researchers, scientists, developers, students – to make neuroscience exciting and accessible for everyone.
And that's why TVB is an open-source project: Codemart wants to share what they know, gain knowledge from other experts and build together a comprehensive infrastructure for studying and treating brain diseases.
TVB on the EBRAINS platform
Since collaboration is key in the open-source world, TVB has officially joined EU’s Human Brain Project in April 2018, which meant that even more people had access to Codemart's work.
Fast forward to 2020 and Codemart's brain simulator was made available on the EBRAINS platform, which offers data, tools and resources for neurostudies.
During the EBRAINS era new auxiliary modules were created to facilitate the usage of TVB from within the EBRAINS infrastructure, specifically from within the official EBRAINS JupyterLab.
This is where Xpress AI and Xircuits came into picture.
Creating TVB simulations with Xircuits
While TVB is a powerful tool for simulating the brain, Codemart wanted to streamline the setup of a simulation as much as possible.
They realised that creating a simulation is very similar to creating workflows: you need to configure several components (model, integrator, coupling, etc.) before feeding them to a big Simulator component. So Codemart started searching for a tool that creates workflows and in JupyterLab.
In 2022 they found Xircuits: a “visual programming environment for JupyterLab”, developed by XpressAI. What you can basically do is drag-and-drop components, create workflows and run them. From a technical point of view, this is a JupyterLab extension, built using React and Python.
At first they created a PoC – they wanted to see if they can adapt this tool to run TVB simulations. The PoC was a big success! Not only were they creating and running simulations with this tool – it also looked pretty cool!
tvb-ext-xircuits: the best of both worlds
Codemart soon realised that they wanted to adapt Xircuits to their custom use-cases. That’s how a new module, called tvb-ext-xircuits, came to life.
They forked the original Xircuits repository and got to work, adding new features focused on interacting with EBRAINS resources – to name a few:
Feature: running a simulation on a remote HPC system and saving the results on the EBRAINS Drive and Bucket
Feature: visualizing components (models) and results (time series) with just 1 click
Feature: description boxes for all custom TVB components and their respective parameters
EBRAINS's own wiki has ample information about this tool and all the others developed for interacting with the EBRAINS platform.
tvb-ext-xircuits is already deployed on the EBRAINS infrastructure and Codemart is currently working on deploying it on the JSC platform from the Jülich Supercomputing Centre.
Strengthening Codemart's collaboration with Xpress AI
From the beginning, the XpressAI team was open to collaboration and Codemart even had a PR merged into the official Xircuits repo!
In addition, there were times when Codemart needed XpressAI's help implementing some custom changes and XpressAI were always eager and quick to offer their support.
And in November 2024 Codemart had the first TVB-Xircuits meeting where they discussed processes to strengthen and evolve this collaboration, making both projects better for their individual user bases.
Acknowledgments
Copyright (c) 2022-2025 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- 2025 to Codemart - Brainiacs team for further changes in this fork.
This extension is build on top of the Xircuits Jupyter extension, and it adds custom features, tailored for EBRAINS and VBT environments.
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).