The Virtual Brain

Cutting-edge brain simulation.

For laptops, servers and clusters.

What you need in a nutshell:

    • Any recent Mac or PC is fine.
    • Supports servers and HPC clusters
    • Works with recent Windows, Mac OS X and Linux
    • Works with modern browsers
    • Allows unlimited users and sharing
    • It's open source and free

Modern hardware: Macs, PCs, servers and HPC clusters

As The Virtual Brain pushes the envelope of practical brain simulation, the hardware you use should be fairly modern. However, the software scales automatically with your needs and resources:

  • One CPU core is needed for one simulation. If you launch more simulations than the number of available CPU cores, we recommend serialization: this can be done by setting the “maximum number of parallel threads” (in the software settings) to the same value as the number of CPU cores.
  • For a single, region-level simulation, 8 GB of RAM should be sufficient. We recommend at least 16 GB of RAM, especially if you intend to run more complex simulations. Surface-level simulations require even more RAM, going up with the number of vertices.
  • Simulating only 10 ms of brain activity on a surface level may occupy around 300 MB of disk space. Basically, we recommend a minimum of 50 GB disk space per user as a rough approximation.
  • Many visualizers display high-resolution graphics. Your monitor should be capable of displaying at least 1600 x 1000 pixels, otherwise some views will be truncated.

If you install TVB on a server, you can share it with an unlimited number of other users and mitigate some of these hardware requirements:

  • Installing TVB in a client/server configuration delegates the hardware requirements for visualization to the client. The server only conducts the operations for simulations and analysis, so it doesn't need powerful graphics hardware. Client access can be established by simply pointing the browser to the URL of the TVB server, e.g. http://tvbserver.mydomain.com:8080

  • The cluster installation is quite similar to the server installation. Please note that SLURM is expected to be configured separately from TVB and accessible to the user for which the TVB software is launched.

    On Human Brain Project infrastructure, the TVB software works with the Red Hat OpenShift platform.

Please have a look at our documentation website, where we go into great detail about various configuration options.

Modern software: Many platforms, all major browsers

Operating systems

  • The current version of TVB was tested on Windows 10. It might still work fine on other versions, as long as they are x64. The installer package was generated on top of an Anaconda Installation.
  • The Mac version was tested on macOS 11.6 but should also run smoothly on small variations from this version.
  • The Linux version was tested on Debian and Fedora. You need to have installed a glibc version of 2.14 or higher. The package was generated on top of an Anaconda Installation.

Browsers

We've tested the software on the latest versions of Google Chrome, Mozilla Firefox and Apple Safari. Using a different, less capable browser might result in some features not working or the user interface looking awkward at times.

Optional: MatLab or Octave

A special feature in TVB is utilizing functions from the Brain Connectivity Toolbox. This feature thus requires a MatLab or Octave package on your computer (installed, activated and added to your OS' global PATH variable).

The Brain Connectivity Toolbox doesn't need to be installed or enabled separately in any way, as TVB will temporarily append it to your MatLab/Octave path.

Software licenses

The Virtual Brain software itself is open source with a GPLv3 license. You can look at the source code for the TVB software GitHub.

For your convenience, we include a number of 3rd-party packages within the TVB software. These packages are not licensed under the TVB software license but remain under their respective licenses (mostly BSD and MIT style).

You find a list of these packages below, including links to their respective project website and license agreement.

Included 3rd-party packages

  • Brain Connectivity Toolbox (BCT)

    This library is distributed with TVB's package, user will need to separately install Matlab in order to make us of its code.

    Version: 0.5.2

    License: GPLv3

    Usage: static linking

    Copyright (c) 2009 Indiana University

  • Connectome File Format Library (cfflib)

    Version: 2.0.5

    License:

    Usage: dynamic linking

    Copyright (C) 2009-2011, Ecole Polytechnique Federale de Lausanne (EPFL) and Hospital Center and University of Lausanne (UNIL-CHUV), Switzerland

  • CherryPy Server

    We use this library for web server.

    Version: 3.8.0,10.2.1

    License: BSD

    Usage: dynamic linking

    Copyright (c) 2002-2008, CherryPy Team (team@cherrypy.org)

  • PyObjC

    We use this library for the Mac OS TVB distribution to appear in the doc bar.

    Version: -

    License: MIT

    Usage: dynamic linking

    Copyright (c) Ronald Oussoren

  • CTypes

    Version: 1.1.0

    License: MIT

    Usage: dynamic linking

    Copyright (c) 2000 - 2006 Thomas Heller

  • D3 JS

    JS library.

    Version: 2

    License: BSD

    Usage: dynamic linking

    Copyright (c) 2012, Michael Bostock

  • Flot

    JS library.

    Version: 0.8.2

    License: MIT

    Usage: dynamic linking

    Copyright (c) 2007-2009 IOLA and Ole Laursen

  • Formencode

    This is a validation and form generation package.

    Version: 1.2.4

    License: PSF

    Usage: dynamic linking

    Copyright 2008-2011, Ian Bicking and Contributors.**

  • Genshi

    Templating library for HTML pages.

    Version: 0.7, 0.6

    License:

    Usage: dynamic linking

    Copyright 2006-2011 Edgewall Software

  • GenXmlIf

    Generic XML interface package

    Version: -

    License: MIT

    Usage: dynamic linking

    Copyright (c) 2005-2008 by Roland Leuthe

  • H5py

    H5Py is the lbrary that we use for accessing from python hdf5 library.

    Version: 2.6.0

    License: BSD

    Usage: dynamic linking

    Copyright (c) 2008 Andrew Collette

  • HDF5 library

    Library used for efficient storage.

    Version: 1.8.17

    License: BSD

    Usage: dynamic linking

    Copyright 2006-2011 by The HDF Group. Copyright 1998-2006 by the Board of Trustees of the University of Illinois.

  • PIL Library

    This library is used when generating TVB documentation

    Version: 1.1.7

    License:

    Usage: documentation

    Copyright (c) 1997-2011 by Secret Labs AB Copyright (c) 1995-2011 by Fredrik Lundh

  • Jit

    JS library.

    Version: 2.0.1

    License: MIT

    Usage: dynamic linking

    Copyright (c) 2010, Nicolas Garcia Belmonte

  • JQuery

    We may use any jQuery project under the terms of either the MIT License or the GNU General Public License (GPL) Version 2. The MIT License is recommended for most projects. It is simple and easy to understand and it places almost no restrictions on what we can do with a jQuery project.

    Version: 2.1.1

    License: MIT

    Usage: dynamic linking

    Copyright (c) 2011 John Resig, http://jquery.com/

  • ATLAS computation library

    Computations library used by numpy.

    Version: -

    License: BSD

    Usage: dynamic linking

    (C) Copyright 1999 R. Clint Whaley

  • BZ2

    LibBZ2 is indirrectly used by the HDF5 libraries.

    Version: -

    License: BSD

    Usage: dynamic linking

    Copyright (C) 1996-2010 Julian Seward

  • Free Type

    A Free, High-Quality, and Portable Font Engine.

    Version: -

    License: BSD

    Usage: dynamic linking

    Copyright 1996-2002, 2006 by David Turner, Robert Wilhelm, and Werner Lemberg

  • MIT Kerberos v5 library

    A dependency of psycopg2 dynamic build. Headers and development libraries for MIT Kerberos.

    Version: -

    License: MIT

    Usage: dynamic linking

    Copyright (C) 1985-2006 by the Massachusetts Institute of Technology.

  • Lapack library

    Numpy linear uses the lapack library for computations.

    Version: -

    License: BSD

    Usage: dynamic linking

    Copyright (c) 1992-2011 The University of Tennessee and The University of Tennessee Research Foundation. All rights reserved.\ Copyright (c) 2000-2011 The University of California Berkeley. All rights reserved.\ Copyright (c) 2006-2011 The University of Colorado Denver. All rights reserved.

  • PNG library

    LIBPNG is the official PNG reference library. Is is included because Matplotlib makes use of it.

    Version: -

    License:

    Usage: dynamic linking

    Copyright (c) 2004, 2006-2012 Glenn Randers-Pehrson

  • TCL85 dylib

    License found at http://www.tcl.tk/software/tcltk/license.html. Library used as IDLE dependency, for the console-users.

    Version: -

    License:

    Usage: dynamic linking

    Copyright (C) 2001 by ActiveState Corporation

  • TCL85 so

    License found at http://www.tcl.tk/software/tcltk/license.html. Library used as IDLE dependency, for the console-users.

    Version: -

    License:

    Usage: dynamic linking

    Copyright (C) 2001 by ActiveState Corporation

  • TK85 dylib

    License found at http://www.tcl.tk/software/tcltk/license.html. Library used as IDLE dependency, for the console-users.

    Version: -

    License:

    Usage: dynamic linking

    Copyright (C) 2001 by ActiveState Corporation

  • TK85 so

    License found at http://www.tcl.tk/software/tcltk/license.html. Library used as IDLE dependency, for the console-users.

    Version: -

    License:

    Usage: dynamic linking

    Copyright (C) 2001 by ActiveState Corporation

  • MathJax

    This library is used to show math formulas in a nicer format.

    Version: 2.0

    License:

    Usage: dynamic linking

  • MatPlotLib

    Version: 1.5.1

    License:

    Usage: dynamic linking

    Copyright (c) 2002-2009 John D. Hunter; All Rights Reserved

  • Migrate SQL Alchemy

    SQLAlchemy related package, for updating from one version of DB to another.

    Version: 0.7.2

    License: MIT

    Usage: dynamic linking

    Copyright (c) 2009 Evan Rosson, Jan Dittberner, Domen Kozar

  • MatPlotLib Toolkits

    This package is part of Matplotlib.

    Version: -

    License:

    Usage: dynamic linking

    Copyright (c) 2002-2009 John D. Hunter; All Rights Reserved

  • NetworkX

    Version: 1.11

    License:

    Usage: dynamic linking

    Copyright (C) 2004-2011, NetworkX Developers Aric Hagberg Dan Schult Pieter Swart

  • Nibabel

    Version: 2.1.0

    License: MIT

    Usage: dynamic linking

    Copyright (c) 2006-2010 Michael Hanke Copyright (c) 2009-2010 Matthew Brett

  • NumExpr

    Fast numerical array expression evaluator for Python and NumPy.

    Version: 2.6.2

    License: MIT

    Usage: dynamic linking

    Copyright (c) 2007,2008 David M. Cooke Copyright (c) 2009,2010 Francesc Alted Copyright (c) 2011- See AUTHORS.txt

  • Numpy

    Numpy library will be used by simulation and analysis modules.

    Version: 1.12.1

    License: BSD

    Usage: dynamic linking

    Copyright (c) 2005-2009, NumPy Developers.

  • Python OpenSSL

    Package part of Python's distribution.

    Version: -

    License: BSD

    Usage: dynamic linking

    Copyright (c) 1998-2008 The OpenSSL Project. All rights reserved.

  • Pillow Library

    This library is used when generating TVB documentation

    Version: 2.9.0

    License:

    Usage: documentation

    Copyright (c) 1997-2011 by Secret Labs AB Copyright (c) 1995-2011 by Fredrik Lundh

  • psutil

    psutil is a module providing an interface for retrieving information on all running processes and system utilization.

    Version: 5.2.2

    License: BSD

    Usage: dynamic linking

    Copyright (c) 2009, Jay Loden, Dave Daeschler, Giampaolo Rodola

  • Psycopg2

    Psycopg is the most popular PostgreSQL adapter for the Python programming language. It has a choosable license (LGPL v3 or BSD Like) and we choose the BSD like one.

    Version: 2.7.1

    License:

    Usage: dynamic linking

    Copyright (c) 2010 - Daniele Varrazzo

  • Python

    Most of TVB code will probably be in Python. Multiple Python libraries, some of them listed below, use Python Software Foundation

    Version: 3.10

    License: PSF

    Usage: dynamic linking

    Copyright (c) 1990-2012, Python Software Foundation.

  • PyTZ: TimeZone Library for Python

    Version: 2017.2

    License: MIT

    Usage: dynamic linking

    Copyright (c) 2003-2009 Stuart Bishop

  • Scipy

    SciPy is freely available. It is distributed as Open Source software, meaning that you have complete access to the source code and can use it in anyway allowed by its liberal BSD_ license.

    Version: 0.19.0

    License: BSD

    Usage: dynamic linking

    Copyright (c) 2001, 2002 Enthought, Inc. Copyright (c) 2003-2009 SciPy Developers.

  • Simple JSON

    Library for JSON encoding/decoding

    Version: 3.10

    License: MIT

    Usage: dynamic linking

    Copyright (c) 2006 Bob Ippolito

  • Scikit Learn

    Version: 0.18.1

    License:

    Usage: dynamic linkingd

    Copyright (c) 2007 - 2012 The scikit-learn developers.

  • SQL-Alchemy

    SQLAlchemy and its documentation are licensed under the MIT_ license.

    Version: 0.7.8

    License: MIT

    Usage: dynamic linking

    Copyright (c) 2005-2011 the SQLAlchemy authors and contributors . SQLAlchemy is a trademark of Michael Bayer.

  • Sqlite DB for Python

    Simple file-based DB.

    Version: 2.6.0

    License: MIT

    Usage: dynamic linking

    Copyright (c) 2004-2007 Gerhard Haring

  • PyTables

    Open source software, under BSD_ license.

    Version: 3.0,3.3

    License: BSD

    Usage: dynamic linking

    Copyright Notice and Statement for PyTables Software Library and Utilities: Copyright (c) 2002-2004 by Francesc Alted Copyright (c) 2005-2007 by Carabos Coop. V. Copyright (c) 2008-2010 by Francesc Alted

  • TCL85 Framework

    License found at http://www.tcl.tk/software/tcltk/license.html. Library used as IDLE dependency, for the console-users.

    Version: -

    License:

    Usage: dynamic linking

    Copyright (C) 2001 by ActiveState Corporation

  • TCL85 dll

    License found at http://www.tcl.tk/software/tcltk/license.html. Library used as IDLE dependency, for the console-users.

    Version: 8.5.2.2

    License:

    Usage: dynamic linking

    Copyright (C) 2001 by ActiveState Corporation

  • Tempita

    This is a dependency of SQLAlchemy's migrate versioning.

    Version: 0.5.2

    License:

    Usage: dynamic linking

    Copyright (c) 2008 Ian Bicking and Contributors

  • TK85 Framework

    License found at http://www.tcl.tk/software/tcltk/license.html. Library used as IDLE dependency, for the console-users.

    Version: -

    License:

    Usage: dynamic linking

    Copyright (C) 2001 by ActiveState Corporation

  • TK85 dll

    License found at http://www.tcl.tk/software/tcltk/license.html. Library used as IDLE dependency, for the console-users.

    Version: 8.5.2.2

    License:

    Usage: dynamic linking

    Copyright (C) 2001 by ActiveState Corporation

  • Python module wsgiref

    The Web Server Gateway Interface (WSGI) is a standard interface between web server software and web applications written in Python.

    Version: 0.1.2

    License: PSF

    Usage: dynamic linking

    Copyright Phillip J. Eby **

  • Python ZLIB

    Package part of Python's distribution.

    Version: 1.0

    License:

    Usage: dynamic linking

    Copyright (C) 1995-2010 Jean-loup Gailly and Mark Adler

  • Anaconda

    Anaconda - Python environment for convenience in setting-up the build machine.

    Version: 4.2

    License: MIT

    Usage: dynamic linking

    Copyright (c) Continuum Analytics Inc

  • IPython

    This library is used for TVB command access

    Version: 5.3.0

    License: BSD

    Usage: dynamic linking

    Copyright (c) 2011, IPython Development Team

  • Zeromq

    The IPython Notebook requires ZeroMQ for communication - Coming with Anaconda env

    Version: 16.0.2

    License: LGPLv3

    Usage: dynamic link

    Copyright (C) 2007-2014 iMatix Corporation and Contributors

  • Zope

    IPython Notebook uses it

    Version: unknown

    License:

    Usage: dynamic link

    Copyright (c) 2012, Zope Foundation contributors

  • Tornado

    The IPython Notebook uses the Tornado project for its HTTP server - Coming with Anaconda env

    Version: 4.5

    License: Apache

    Usage: dynamic link

    Copyright (c) 2011, Facebook.

  • Markupsafe

    The IPython Notebook uses the MarkupSafe - Coming with Anaconda env

    Version: 0.23,1.0

    License: BSD

    Usage: dynamic link

    Copyright (c) 2010 by Armin Ronacher and contributors. See AUTHORS for more details.

  • Jinja

    IPython Notebook uses the Jinja templating tool to render HTML pages

    Version: 2.8

    License: BSD

    Usage: dynamic linking

    Copyright (c) 2009 by the Jinja Team

  • Functools32

    The IPython Notebook uses it

    Version: 3.2.3-2

    License: PSF

    Usage: dynamic linking

    Copyright (c) 2010-2012, ENDOH takanao

  • Concurrent

    Coming with Anaconda env

    Version: unknown

    License: BSD

    Usage: dynamic linking

    Copyright (c) 2009 Brian Quinlan. All rights reserved.

  • Certifi

    Used by IPython Notebook - Coming with Anaconda env

    Version: 2017.04.17,14.5.14

    License: ISC

    Usage: dynamic linking

    Copyright (c) 2015 Kenneth Reitz

  • Beautiful Soup (BS4)

    Tree Parser - Coming with Anaconda env

    Version: 4.3.2,4.6.0

    License: MIT

    Usage: dynamic linking

    Copyright (c) 2004-2012 Leonard Richardson

  • AllenSDK

    AllenSDK is used for connecting from TVB to Allen DB

    Version: 0.12.4

    License: GPLv3

    Usage: dynamic linking

    Copyright 2015-2016 Allen Institute for Brain Science

  • Pandas

    Package needed for AllenSDK

    Version: 0.18.1

    License: BSD

    Usage: dynamic linking

    Copyright (c) 2011-2012, Lambda Foundry, Inc. and PyData Development Team

  • Cheroot

    Highly-optimized, pure-python HTTP server. Used by CherryPy

    Version: 5.5.0

    License: BSD

    Usage: dynamic linking

    Copyright (c) 2004-2016, CherryPy Team (team@cherrypy.org)

  • Colorama

    Cross-platform colored terminal text.

    Version: 0.3.7

    License: BSD

    Usage: dynamic linking

    Copyright (c) 2010 Jonathan Hartley

  • GFortran dylib

    The GNU Fortran compiler, part of GCC. Needed by recent numpy.

    Version: -

    License: GPLv2

    Usage: dynamic linking

    Copyright (C) 1999-2016 Free Software Foundation, Inc.

  • GCC Quad-Precision Math Library Application Programming Interface (API)

    Version: -

    License: GPLv2

    Usage: dynamic linking

    Copyright (C) 2010, 2011 Free Software Foundation, Inc.