This is the examples directory for the Brain Modeling Toolkit (bmtk) software package. Here you will find examples of how to build, simulate, and plot simple brain network models of a variety of different levels-of-resolution using bmtk. These examples are toy models for demonstration of how to use bmtk capable of running on a laptop/desktop machine (for some examples of scientifically developed models that run on bmtk please see the following link: https://alleninstitute.github.io/bmtk/examples.html).

Each bio_*/ directory uses the BioNet simulator to run morphologically detailed network simulations using the NEURON simulation tool.

bio_components/ contains external parameter and model files which are shared by most of the BioNet examples (note: this location can be changed in the each example's config.circuit.json file). This also includes a bio_components/mechanism/ directory which require extra compilation for the Allen Institute models. To run the BioNet examples one will have to run the following commands to compile the extra neuronal mechanisms:

$ cd examples/bio_components/mechanisms
$ nrnivmodl modfiles

For more information on using BioNet see the following: https://alleninstitute.github.io/bmtk/bionet.html

point_*/ directories contain examples that use the PointNet simulator to run point-neuron type models, including Allen Institute's Generalized Integrate-and-Fire (GLIF) models. Using these examples will require installing the NEST simulator.

point_components/ directory contains model files that are shared by many of the different PointNet examples. This can be changed in each examples' config.circuit.json files.

For more information on using PointNet see the following: https://alleninstitute.github.io/bmtk/pointnet.html

pop_*/directories contain examples that use the PopNet simulator to run population level firing-rate model simulations. This requires installing the DiPDE simulator.

pop_components/ directory contains model files that are shared by many of the different PopNet examples. This can be changed in each examples' config.circuit.json files.

For more information on using PopNet see the following: https://alleninstitute.github.io/bmtk/popnet.html

filter_*/ directories contain examples that use the PopNet simulator to run filter models simulations to convert visual stimuli into spike-trains.

filter_components/ directory contains model files that are shared by many of the different FilterNet examples. This can be changed in each examples' config.circuit.json files.

For more information on using PopNet see the following: https://alleninstitute.github.io/bmtk/filternet.html