title: Integrating neuroinformatics tools in TheVirtualBrain.
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 and 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.
authors.affiliation: Institut National de la Santé et de la Recherche Médicale UMR 1106, Institut de Neurosciences des Systèmes Marseille, France ; Institut de Neurosciences des Systèmes, Aix-Marseille Université Marseille, France.
authors.forename: M Marmaduke
authors.initials: MM
authors.lastname: Woodman
authors.affiliation: Institut National de la Santé et de la Recherche Médicale UMR 1106, Institut de Neurosciences des Systèmes Marseille, France ; Institut de Neurosciences des Systèmes, Aix-Marseille Université Marseille, France.
authors.forename: Laurent
authors.initials: L
authors.lastname: Pezard
authors.affiliation: Codemart Cluj-Napoca, Romania.
authors.forename: Lia
authors.initials: L
authors.lastname: Domide
authors.affiliation: Institut National de la Santé et de la Recherche Médicale UMR 1106, Institut de Neurosciences des Systèmes Marseille, France ; Institut de Neurosciences des Systèmes, Aix-Marseille Université Marseille, France.
authors.forename: Stuart A
authors.initials: SA
authors.lastname: Knock
authors.affiliation: Institut National de la Santé et de la Recherche Médicale UMR 1106, Institut de Neurosciences des Systèmes Marseille, France ; Institut de Neurosciences des Systèmes, Aix-Marseille Université Marseille, France.
authors.forename: Paula
authors.initials: P
authors.lastname: Sanz-Leon
authors.affiliation: CodeBox GmbH Stuttgart, Germany.
authors.forename: Jochen
authors.initials: J
authors.lastname: Mersmann
authors.affiliation: Rotman Research Institute at Baycrest Toronto, ON, Canada.
authors.forename: Anthony R
authors.initials: AR
authors.lastname: McIntosh
authors.affiliation: Institut National de la Santé et de la Recherche Médicale UMR 1106, Institut de Neurosciences des Systèmes Marseille, France ; Institut de Neurosciences des Systèmes, Aix-Marseille Université Marseille, France.
authors.forename: Viktor
authors.initials: V
authors.lastname: Jirsa
keywords: Python; brain networks; connectivity; electroencephalography; functional MRI; magnetoencephalography; neural mass; time delays