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Welcome to DynaSim!

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. DynaSim supports arbitrarily complex population models and networks of interconnected populations. The toolbox 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 includes a graphical user interface (DynaSim GUI) that supports full functionality without requiring user programming.

If you use DynaSim for your published research, please cite this introductory article:

Sherfey JS, Soplata AE, Ardid S, Roberts EA, Stanley DA, Pittman-Polletta BR and Kopell NJ (2018) DynaSim: A MATLAB Toolbox for Neural Modeling and Simulation. Front. Neuroinform. 12:10. doi: 10.3389/fninf.2018.00010

See the DynaSim Toolbox in action, with Getting started tutorial and the UnbiasedCompetition demonstration live script.

Documentation

• Installation
• Tutorials
  • Getting started with DynaSim
  • Graphical User Interface (GUI) Tutorial
  • High performance computing
  • Multi-compartment and large network models
  • Combining models
  • Using predefined populations
  • Making predefined populations
  • Using custom models and mechanisms
  • Global sensitivity analysis for PBPK modeling
• Live Script Tutorials
  • Striatal Unbiased Competition Model (m-file)
  • Frontoparietal rate models of working memory and decision making (m-file)
  • Network resonance in prefrontal cortex (m-file)
• Examples
  • Monitoring spikes, LIF networks, and STDP
  • Using the iPoisson input mechanism
  • Delay differential equations
  • Model Specification Using Equation Strings
  • Harmonic oscillators
  • 2D Reaction-diffusion equations
  • 2D Shunting network
  • Cortical network with multicompartment neurons (repository)
  • Thalamic TC/RE model (Soplata et al., 2017) (deprecated)
  • Thalamocortical model (Krishnan et al., 2016) (deprecated)
• Reference
  • Function Reference
  • Option Reference
  • Data Structure Reference
  • Mechanism File Precedence Order
• Best Practices and FAQ
  • Best Practices
  • Frequently Asked Questions

Support

• How to get the most effective support:
  • Join the user mailing list to ask questions and discuss DynaSim.
  • Report code bugs and feature requests on the issues page.
• Troubleshooting
• MATLAB support in DynaSim
• GNU Octave support in DynaSim

Developers

• Developer Central