Frontiers in Neuroinformatics (Apr 2014)
Integrating neuroinformatics tools in TheVirtualBrain
Abstract
TheVirtualBrain (TVB) is a neuroinformatics Python package representing theconvergence of clinical, systems, and theoretical neuroscience in the analysis,visualization and modeling of neural and neuroimaging dynamics. TVB iscomposed of a flexible simulator for neural dynamics measured across scalesfrom local populations to large-scale dynamics measured byelectroencephalography (EEG), magnetoencephalography (MEG) and functionalmagnetic resonance imaging (fMRI), and core analytic and visualizationfunctions, all accessible through a web browser user interface. A datatypesystem modeling neuroscientific data ties together these pieces with persistentdata storage, based on a combination of SQL & HDF5. These datatypes combinewith adapters allowing TVB to integrate other algorithms or computationalsystems. TVB provides infrastructure for multiple projects and multiple users,possibly participating under multiple roles. For example, a clinician mightimport patient data to identify several potential lesion points in thepatient's connectome. A modeler, working on the same project, tests thesepoints for viability through whole brain simulation, based on the patient'sconnectome, and subsequent analysis of dynamical features. TVB also drivesresearch forward: the simulator itself represents the culmination of severalsimulation frameworks in the modeling literature. The availability of thenumerical methods, set of neural mass models and forward solutions allows forthe construction of a wide range of brain-scale simulation scenarios. Thispaper briefly outlines the history and motivation for TVB, describing theframework and simulator, giving usage examples in the web UI and Pythonscripting.
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