AUTHOR=Woodman M. Marmaduke , Pezard Laurent , Domide Lia , Knock Stuart A. , Sanz-Leon Paula , Mersmann Jochen , McIntosh Anthony R. , Jirsa Viktor TITLE=Integrating neuroinformatics tools in TheVirtualBrain JOURNAL=Frontiers in Neuroinformatics VOLUME=Volume 8 - 2014 YEAR=2014 URL=https://www.frontiersin.org/journals/neuroinformatics/articles/10.3389/fninf.2014.00036 DOI=10.3389/fninf.2014.00036 ISSN=1662-5196 ABSTRACT=TheVirtualBrain (TVB) is a neuroinformatics Python package representing the
convergence of clinical, systems, and theoretical neuroscience in the analysis,
visualization and modeling of neural and neuroimaging dynamics. TVB is
composed of a flexible simulator for neural dynamics measured across scales
from local populations to large-scale dynamics measured by
electroencephalography (EEG), magnetoencephalography (MEG) and functional
magnetic resonance imaging (fMRI), and core analytic and visualization
functions, all accessible through a web browser user interface. A datatype
system modeling neuroscientific data ties together these pieces with persistent
data storage, based on a combination of SQL \& HDF5. These datatypes combine
with adapters allowing TVB to integrate other algorithms or computational
systems. TVB provides infrastructure for multiple projects and multiple users,
possibly participating under multiple roles. For example, a clinician might
import patient data to identify several potential lesion points in the
patient's connectome. A modeler, working on the same project, tests these
points for viability through whole brain simulation, based on the patient's
connectome, and subsequent analysis of dynamical features. TVB also drives
research forward: the simulator itself represents the culmination of several
simulation frameworks in the modeling literature. The availability of the
numerical methods, set of neural mass models and forward solutions allows for
the construction of a wide range of brain-scale simulation scenarios. This
paper briefly outlines the history and motivation for TVB, describing the
framework and simulator, giving usage examples in the web UI and Python
scripting.