Simulation

The Virtual Brain

End-to-end workflow for creating personalised brain models and simulating multi-scale networks with The Virtual Brain


The Virtual Brain In EBRAINS

Use The Virtual Brain to construct personalized brain models and simulate them.

Construct virtual brains from your own individual brain scans by running available processing pipelines on high performance computers on CSCS

Use processed The-Virtual-Brain ready brain scans to run your simulations. Simulate the brain at multiple scales.

Use optimized Virtual Brain code for high performance computing and enjoy various training materials on INCF training space.

Virtual Brain integrated EBRAINS tools and workflows

The Virtual Brain (TVB) is an open source platform for constructing and simulating personalised brain network models. It is available as standalone version from this website thevirtualbrain.org

End-to-end workflow for creating personalised brain models to running multi-scale brain simulations with The Virtual Brain are now available as integrated software solutions on the EBRAINS cloud.

• Find TVB tools and data via the Knowledge Graph
• Use TVB workflows via the Collaboratory
• Run TVB workflows in the EBRAINS Cloud or on HPC backend

Integrated TVB workflows on EBRAINS enable the processing of large cohort data sets - solving the problem of small numbers preventing generalizable results, a precondition for clinical translation.

Access the Integrated TVB Workflows

The software can be used remotely from your local computer with the TVB EBRAINS Web App GUI, making computationally expensive neurological research possible from the comfort of your web browser.

Create simulation-ready brain models and derivatives with THE VIRTUAL BRAIN PIPELINE

TVB Reference Data on EBRAINS

  • Use your own data to create simulation-ready brain models.
  • Find published brain models and derivatives in BIDS format with the EBRAINS Knowledge Graph.
  • Access published models and derivatives annotated with metadata from
    EBRAINS repositories, e.g.
    • clinical data from brain tumour patients
    • ADNI Alzheimer’s BIDS-compliant derivatives (published by end of January 2020)
  • Use processed TVB ready brain scans to run your simulations

Personalised brain model

  • Create personalised brain network models from MRI, PET and M/EEG data using TVB’s state of the art neuroimaging pipeline.
  • Compute structural and functional connectomes and source-level M/EEG.
  • Take advantage of a variety of BIDS Apps deployed on Swiss supercomputing centre CSCS that can be conveniently operated from the Collaboratory web interface.
  • Make your brain models and derivatives findable and citable with the EBRAINS Knowledge Graph and persistent DOIs.
  • Constrain virtual brains with The Virtual Brain ready data derivatives in BIDS format.
  • Construct virtual brains from your own individual brain scans by running available processing pipelines on high performance computers on FENIX.

Simulate and analyse large-scale brain network models with TVB-SIMULATOR

Brain simulation

  • Run The Virtual Brain neuroinformatics platform graphical user interface from HBP Collabs to simulate brain models and analyze results.
  • Take advantage of supercomputing ressources at CSCS to perform parameter space explorations.
  • Use and re-use Jupyter notebooks for efficient creation, simulation and analysis of brain simulations via The Virtual Brain’s programmatic interface.
  • Enjoy the video tutorial platform EduPack to quickly get acquainted with TVB technologies.
  • Use The Virtual Brain to construct personalized brain models and simulate them
  • Use The-Virtual-Brain EBRAINS Web App GUI or command line for simulating and analysing large-scale brain network dynamics based on biologically realistic connectivityin the EBRAINS Cloud

Increase detail by coupling large-scale brain models with spiking networks using TVB-NEST cosimulation

Multiscale simulation

  • Study the impact of realistic large-scale brain network activity on spiking neurons and networks.
  • Replace entire brain areas by spiking networks and study emerging mean field dynamics.
  • Quickly set up multiscale models with a convenient Python wrapper that integrates The Virtual Brain and NEST interfaces.
     

Increase simulation speed using FAST-TVB

High performance simulation

  • Perform extensive parameter space explorations or faster than realtime simulations of large networks with FAST-TVB.
  • Exploit parallel supercomputing architectures with multithreaded The Virtual Brain simulations.
  • Use a convenient platform-independent Docker container on your computer, supercomputer or at CSCS.
  • Use optimized Virtual Brain code for high performance computing
     

Visualise brain parcellations and simulation results with TVB-ATLAS

Brain atlas

  • Explore brain parcellations and the functional relevance of different brain areas.
  • Learn the location and shape of areas, selectable by anatomy or function.
  • Descriptions are available in English, Arabic, Hebrew, and German.
     

A TVB User Story

From MRI to personalized brain simulation

Here we explain step by step how to use The Virtual Brain (TVB) tools for end-to-end personalized brain simulation. We start by finding shared MRI data using KnowledgeGraph, create a brain model from extracted connectomes using TVB pipeline, and simulate neural activity using TVB brain network model simulators. We will use Jupyter notebooks on EBRAINS Collab platforms for frontend operations and supercomputers in the backend for intensive number crunching.

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