The Virtual Brain
The Virtual Brain (TVB) offers software for constructing, simulating and analysing brain network models including the TVB simulator; magnetic resonance imaging (MRI) processing pipelines to extract structural and functional brain networks; combined simulation of large-scale brain networks with small-scale spiking networks; automatic conversion of user-specified model equations into fast simulation code; simulation-ready brain models of patients and healthy volunteers; Bayesian parameter optimization in epilepsy patient models; data and software for mouse brain simulation; and extensive educational material ([Sanz_Leon_2013], [Schirner_2022]).
Official resources
HIP resources
The following HIP tutorials are available:
The Virtual Brain on the HIP
The Virtual Brain app on the HIP relies on Jupyter notebooks. Starting the app will actually starts JupyterLab Desktop, a cross-platform desktop application for JupyterLab. For additional information regarding Jupyter notebooks, please consult the official documentation.
References
- Sanz_Leon_2013
Sanz Leon P, Knock SA, Woodman MM, Domide L, Mersmann J, McIntosh AR, Jirsa V. The Virtual Brain: a simulator of primate brain network dynamics. Front Neuroinform., 2013, 7:10.
- Schirner_2022
Schirner M, Domide L, Perdikis D, Triebkorn P, Stefanovski L, Pai R, Prodan P, Valean B, Palmer J, Langford C, Blickensdörfer A, van der Vlag M, Diaz-Pier S, Peyser A, Klijn W, Pleiter D, Nahm A, Schmid O, Woodman M, Zehl L, Fousek J, Petkoski S, Kusch L, Hashemi M, Marinazzo D, Mangin JF, Flöel A, Akintoye S, Stahl BC, Cepic M, Johnson E, Deco G, McIntosh AR, Hilgetag CC, Morgan M, Schuller B, Upton A, McMurtrie C, Dickscheid T, Bjaalie JG, Amunts K, Mersmann J, Jirsa V, Ritter P. Brain simulation as a cloud service: The Virtual Brain on EBRAINS. Neuroimage., 2022, 251:118973.