The Brain Dynamics Toolbox is an open-source toolbox for simulating non-linear dynamical systems in Matlab. It is aimed at researchers in computational neuroscience but can be applied to problems in any domain. It specifically solves initial-value problems in systems of Ordinary Differential Equations (ODEs), Delay Differential Equations (DDEs) and Stochastic Differential Equations (SDEs). Each of which can be extended to Partial Differential Equations (PDEs) using the method of lines.
The major benefit of the toolbox is that it allows custom dynamical models to be conveniently investigated at all stages of the research lifecycle. Its graphical interface allows the dynamics to be explored intuitively without the need for graphical programming. New models can typically be written in less than 100 lines of code. Furthermore that source code can be published independently of the toolbox. Once a model is written, the hub-and-spoke architecture of the toolbox 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 a similar number of display panels. Users can augment that list with their own display panels and solver algorithms. The graphical controls are designed so that they can also be manipulated via the Matlab command window. Simple for-loop commands can thus be used to semi-automate parameter surveys and produce bifurcation diagrams with minimal effort. Larger-scale simulations can be fully automated with the command-line tools that are also provided.
The toolbox ships with approximately 30 example models that can be used for teaching or as starting points for building custom models. The software interface is extensively documented in the Handbook for the Brain Dynamics Toolbox which can be purchased in print or digital editions. Chapter 1 can be downloaded for free from the toolbox website at https://bdtoolbox.org.
The website also offers online training courses. These are self-paced courses which demonstrate various methods using short (15 min) video lectures. There are currently two courses on offer. The first is called Toolbox Basics. It is a beginner’s level course that demonstrates how to install the toolbox and run the example models in about 2 hours. The second course is called the Modeller’s Workshop. It is an advanced course for those who wish to build their own dynamical models. Topics include programming systems of ODEs, SDEs, DDEs and PDEs and using the command-line tools. The study time for that course is approximately 8 hours.
The toolbox can itself serve as a teaching tool for traditional courses in dynamical systems. It allows instructors to provide their students with pre-built models that are tailored to their coursework. This frees the students from the implementation burden and allows them to focus on the core dynamical concepts. Students also have the option to customise the example models for project-based learning outcomes.
The Brain Dynamics Toolbox requires Matlab R2014b or newer. It can be downloaded from https://bdtoolbox.org
|ODE, SDE, DDE, neuroscience