The Brain Dynamics Toolbox for Matlab

Nonlinear dynamical systems are increasingly informing both theoretical and empirical branches of neuroscience. The Brain Dynamics Toolbox provides an interactive simulation platform for exploring such systems in MATLAB. It supports the major classes of differential equations that arise in computational neuroscience: Ordinary Differential Equations, Delay Differential Equations and Stochastic Differential Equations. The design of the graphical interface fosters intuitive exploration of the dynamics while still supporting scripted parameter explorations and large-scale simulations. Although the toolbox is intended for dynamical models in computational neuroscience, it can be applied to dynamical systems from any domain.

[1]  Thomas F. Fairgrieve,et al.  AUTO 2000 : CONTINUATION AND BIFURCATION SOFTWARE FOR ORDINARY DIFFERENTIAL EQUATIONS (with HomCont) , 1997 .

[2]  Michael L. Hines,et al.  The NEURON Book , 2006 .

[3]  Romain Brette,et al.  The Brian Simulator , 2009, Front. Neurosci..

[4]  J. Hindmarsh,et al.  A model of neuronal bursting using three coupled first order differential equations , 1984, Proceedings of the Royal Society of London. Series B. Biological Sciences.

[5]  John W. Eaton,et al.  Gnu Octave Manual , 2002 .

[6]  Frank Schilder,et al.  Recipes for Continuation , 2013, Computational science and engineering.

[7]  Rolf Kötter,et al.  Online retrieval, processing, and visualization of primate connectivity data from the CoCoMac Database , 2007, Neuroinformatics.

[8]  Willy Govaerts,et al.  MATCONT: A MATLAB package for numerical bifurcation analysis of ODEs , 2003, TOMS.

[9]  Rustam Singh,et al.  Simulating , 2012 .

[10]  W. Stacey,et al.  On the nature of seizure dynamics. , 2014, Brain : a journal of neurology.

[11]  Donald T. Hawkins Online retrieval , 1987, J. Am. Soc. Inf. Sci..

[12]  Bard Ermentrout,et al.  Simulating, analyzing, and animating dynamical systems - a guide to XPPAUT for researchers and students , 2002, Software, environments, tools.

[13]  H. Haken,et al.  Field Theory of Electromagnetic Brain Activity. , 1996, Physical review letters.

[14]  O. Sporns,et al.  Towards the virtual brain: network modeling of the intact and the damaged brain. , 2010, Archives italiennes de biologie.

[15]  Robert Clewley,et al.  Hybrid Models and Biological Model Reduction with PyDSTool , 2012, PLoS Comput. Biol..

[16]  James M. Bower,et al.  The Book of GENESIS , 1994, Springer New York.