Fenix resources support Simulation as a Service provided by The Virtual Brain

02 Mar 2021

The Fenix infrastructure resources were used to support simulation workflows with The Virtual Brain (TVB), an open-source platform for constructing and simulating personalised brain network models (TVB-on-EBRAINS). TVB has recently been integrated with the core services offered by the European Brain Research INfrastructureS (EBRAINS), a shared digital research platform for brain science. EBRAINS was developed by the Human Brain Project (HBP), a research initiative funded by the European Commission with the mission to decode the human brain.

The TVB-on-EBRAINS ecosystem includes a variety of prepackaged modules, integrated simulation tools, pipelines and data sets for easy and immediate use. Scientists can process their large cohort databases and use these results to develop potential medical treatments, therapies or diagnostic procedures.

Thanks to access to compute and storage resources of the Fenix Research Infrastructure via the ICEI project, TVB-on-EBRAINS workflows exploit the power of supercomputing services and provide the connection of different cloud components, such as authentication, data transfer and supercomputer job scheduling, thus building an integrated cloud ecosystem.

Petra Ritter, Director of the Section Brain Simulation at the Berlin Institute of Health & Charité Universitätsmedizin Berlin and one of the TVB Leaders, says:

"We are delighted to provide Brain Simulation as a Service to the neuroscience community. TVB-on-EBRAINS integrated workflows are the result of a large team effort. The technical integration of complex workflows in the distributed research infrastructure EBRAINS requires the collaboration between many teams. This work was an amazing and very pleasant experience."

In particular, the TVB-on-EBRAINS platform offers:
•    services for constructing, simulating and analysing brain network models (BNMs) including the TVB network simulator
•    magnetic resonance imaging (MRI) processing pipelines to extract structural and functional connectomes
•    multiscale co-simulation of spiking and large-scale networks
•    a domain specific language for automatic high-performance code generation from user-specified models
•    simulation-ready BNMs of patients and healthy volunteers
•    Bayesian inference of epilepsy spread
•    data and code for mouse brain simulation
•    extensive educational material

A significant contribution of TVB is that its cloud services facilitate reproducible online collaboration and discovery of data assets, models, and software embedded in scalable and secure workflows, a precondition for research on large cohort data sets, better generalizability and clinical translation.

An overview of TVB on EBRAINS cloud ecosystem can be seen in the Figure below:

Full details can be found in the following ArXiv manuscript: https://arxiv.org/abs/2102.05888

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Fenix has received funding from the European Union's Horizon 2020 research and innovation programme through the ICEI project under the grant agreement No. 800858.