NeuronetExperimenter Manual
J. A. Hayes and J. L. Mendenhall
The
NeuronetExperimenter software can be used to quickly simulate large
sets of biological neurons arranged with arbitrary network
connectivity. The software makes it easy to investigate the behaviors of large,
complex, neural networks, especially when starting from XPPAUT models. The software is very flexible and
allows users to develop multiple neuron types with different
constituent differential equations describing their behavior. Any of
these neuron types can be included in a network together where each
neuron has its own unique set of parameters that can be changed during
the course of the simulation. The software also includes extensive analysis features useful for studying the behaviors of large networks.
NeuronetExperimenter
can run simulations serially (i.e., on a single CPU), or in parallel
(i.e., on multi-CPU machines or clusters of computers). For the latter
case, simulation integrations are performed in parallel, so special
considerations are required to understand what types of networks will
benefit from parallel processing (see the Parallel Processing of a Network Simulation topic).
The easiest way to get started with this simulator is to walk through the installation guide and then follow the tutorials:
Installation GuideTutorials
Tutorial #1. Building and Running a Simple Single-Neuron Simulation
Tutorial #2. Coupling Neurons through Synaptic Connections
Tutorial #3. Changing Neuronal Parameters Before and During a Simulation
Tutorial #4. Creating Larger Networks and Introducing Parameter Heterogeneity and Variable Connectivity
Tutorial #5. Analysis of Burst Activity
Tutorial #6. Adding Additional Types of Neurons to a Network
Basic Topics
Parallel Processing of a Network Simulation
Sampling of Data Output
Using the Utility Scripts
Useful Environment Variables to Set
Advanced Topics
Advanced Installation Guide
Network Burst Finding algorithm
Additional Information
File Types and Usage.