Format

Send to

Choose Destination
Front Neuroinform. 2018 Mar 15;12:10. doi: 10.3389/fninf.2018.00010. eCollection 2018.

DynaSim: A MATLAB Toolbox for Neural Modeling and Simulation.

Author information

1
Department of Mathematics and Statistics, Boston University, Boston, MA, United States.
2
Center for Systems Neuroscience, Psychological and Brain Sciences, Boston University, Boston, MA, United States.
3
Graduate Program for Neuroscience, Boston University, Boston, MA, United States.
4
Department of Biomedical Engineering, Boston University, Boston, MA, United States.

Abstract

DynaSim is an open-source MATLAB/GNU Octave toolbox for rapid prototyping of neural models and batch simulation management. It is designed to speed up and simplify the process of generating, sharing, and exploring network models of neurons with one or more compartments. Models can be specified by equations directly (similar to XPP or the Brian simulator) or by lists of predefined or custom model components. The higher-level specification supports arbitrarily complex population models and networks of interconnected populations. DynaSim also includes a large set of features that simplify exploring model dynamics over parameter spaces, running simulations in parallel using both multicore processors and high-performance computer clusters, and analyzing and plotting large numbers of simulated data sets in parallel. It also includes a graphical user interface (DynaSim GUI) that supports full functionality without requiring user programming. The software has been implemented in MATLAB to enable advanced neural modeling using MATLAB, given its popularity and a growing interest in modeling neural systems. The design of DynaSim incorporates a novel schema for model specification to facilitate future interoperability with other specifications (e.g., NeuroML, SBML), simulators (e.g., NEURON, Brian, NEST), and web-based applications (e.g., Geppetto) outside MATLAB. DynaSim is freely available at http://dynasimtoolbox.org. This tool promises to reduce barriers for investigating dynamics in large neural models, facilitate collaborative modeling, and complement other tools being developed in the neuroinformatics community.

KEYWORDS:

GNU octave; code generation; code:matlab; dynamical systems; graphical user interface; neural models; neuroscience gateway

Supplemental Content

Full text links

Icon for Frontiers Media SA Icon for PubMed Central
Loading ...
Support Center