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.

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

Data

  • Use your own data to create simulation-ready brain models.
  • Find published brain models and derivatives in BIDS format with 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).
       

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 HBP Collab web interface.
  • Make your brain models and derivatives findable and citable with HBP’s KnowledgeGraph and persistent DOIs.
  • Constrain virtual brains with The Virtual Brain ready data derivatives in BIDS format.
     

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.
     

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.
     

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.
     
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