The Virtual Brain (TVB) on EBRAINS is a large ecosystem of tools for constructing, simulating and analyzing brain network models. The Virtual Brain tool set can be used for end-to-end personalized brain simulation. It is completely integrated in the EBRAINS technical infrastructure.
The Virtual Brain integration in EBRAINS allows users to have a seamless end-to-end experience of personalized brain model creation and multi-scale brain simulation using high-performance computing on the cloud. This makes it possible to process large cohort datasets in order to produce generalized results - a precondition for clinical translation.
The Virtual Brain (TVB) ecosystem includes:
The Virtual Brain pipeline
TVB pipeline is a neuroimaging pipeline that extracts structural and functional connectomes from MRI data to personalize brain models.
TVB+NEST is a Python toolbox that makes it easier to simulate multi-scale networks. Multi-scale networks simulate both activity on a coarse scale and activity on a finer scale. Essentially, TVB+NEST is a Python wrapper for The Virtual Brain neuroinformatics platform and the NEST spiking network simulator.
Fast_TVB is thousands of times faster than Python TVB as it uses several optimization techniques and is implemented in the hardware-near language C. In addition, users can specify the number of threads that will process data simultaneously across multiple processors, as is often done on supercomputers.
An advanced application of TVB is the specification of disease models. This is done using a workflow that augments TVB with empirical PET data.
Tumor Brain Models
Tumor Brain Models is a data set that includes structural and functional connectomes from brain tumor patients and healthy control subjects.
INCF training space
A dedicated INCF training space provides didactic use cases and Jupyter notebooks to get new users up to speed. EduCases demonstrate - for example - how to use TVB via the Collaboratory of the Human Brain Project, how to run multi-scale co-simulations with other simulators such as NEST and how to process imaging data to construct personalized virtual brains of healthy individuals and patients.
The Virtual Brain simulator
The Virtual Brain simulator is the main TVB software package. It is a neuroinformatics platform that provides an ecosystem of tools for simulating and analysing large-scale brain network dynamics based on biologically realistic connectivity. TVB can be operated via GUI and programmatic Python interface. The Virtual brain simulator is accessible via EBRAINS user accounts.
Check out a detailed step by step guide to using The Virtual Brain tools for end-to-end personalized brain simulation here.