Stewart Heitmann S2: The Brain Dynamics Toolbox (https://bdtoolbox.org) is an open-source toolbox for simulating dynamical systems in neuroscience using Matlab. It specifically solves initial-value problems in user-defined systems of Ordinary Differential Equations (ODEs), Delay Differential Equations (DDEs), Stochastic Differential Equations (SDEs) and Partial Differential Equations (PDEs). New models can typically be written in less than 100 lines of code and then applied at all stages of the research lifecycle. Rapid prototyping is done via the graphical interface where the dynamics can be explored interactively without the need for graphical programming. Interactive parameter surveys can then be semi-automated using the Matlab command window. Large-scale simulations can be fully-automated in user-defined scripts.
Once a model is written, the toolbox’s hub-and-spoke architecture allows unlimited combinations of plotting tools (display panels) and solver algorithms to be applied to that model with no additional programming effort. The toolbox currently supports a dozen solvers and display panels. It also ships with approximately 30 example models that can be used for teaching or as starting points for building new models. Online training courses are available from the bdtoolbox.org website. Extensive documentation is provided in the Handbook for the Brain Dynamics Toolbox.
This software showcase aims to introduce the toolbox to a wider audience through a series of real-time demonstrations. The audience will learn how to get started with the toolbox, how to run existing models and how to semi-automate the controls to generate a bifurcation diagram.
Background reading and software tools- https://bdtoolbox.org•
- Heitmann S, Breakspear M (2017-2019) Handbook for the Brain Dynamics Toolbox. QIMR Berghofer Medical Research Institute. 1st Edition: Version 2017c, ISBN 978-1-5497-2070-3. 2nd Edition: Version 2018a, ISBN 978-1-9805-7250-3. 3rd Edition: Version 2018b, ISBN 978-1-7287-8188-4. 4th Edition: Version 2019a, ISBN 978-1-0861-1705-9.
- Heitmann S, Aburn M, Breakspear M (2017) The Brain Dynamics Toolbox for Matlab. Neurocomputing. Vol 315. p82-88. doi:10.1016/j.neucom.2018.06.026.
