Welcome to the Brain Modeling Toolkit

The Brain Modeling Toolkit (BMTK) is a python-based software package for creating and simulating large-scale neural network models. It supports building, simulation and analysis of models of different levels of resolution including:

  • Biophysically detailed networks.
  • Point neuron networks.
  • Filter models.
  • Population-level networks.
_images/levels_of_resolution_noml.png

The BMTK was developed and is supported at the Allen Institute for Brain Science and released under a BSD 3-clause license. We encourage others to use the BMTK for their own research, and suggestions and contributions to the BMTK are welcome.

The latest release, previous releases, and current development can be found at:

https://github.com/AllenInstitute/bmtk

Requirements

The BMTK runs on Python 2.7 and 3.6+. To use the base features, including building and analyzing networks, the following numpy packages are required. When installing using anaconda, pypi or distutils these dependencies will be installed if not already:

Optional dependencies:

For running network simulations BMTK uses existing software, which will differ depending on the type of simulation. As such there may be additional requirements.

neuron_icon Biophysically detailed simulation with BioNet uses the NEURON simulator (7.4+)

nest_icon Point simulations with PointNet uses the NEST simulator (2.11+)

dipde_icon Population level firing rates simulation with PopNet uses DiPDE

FilterNet Filter models with LGNModel uses

See Installation page and individual simulator pages for further instructions.

Additional Resources

Tutorials - Jupyter-notebook tutorials for using the BMTK can be found at https://github.com/AllenInstitute/bmtk/blob/develop/docs/tutorial/00_introduction.ipynb.

Examples - A collection of examples for building and running simulations across different levels of resolution can be found at https://github.com/AllenInstitute/bmtk/tree/develop/docs/examples.

Questions - Any bugs, questions, or feature requests can be done from our github issue page at https://github.com/AllenInstitute/bmtk/issues. Or please feel free to contact Anton Arkhipov (antona at alleninstitute dot org) and Kael Dai (kaeld at alleninstitute dot org) regarding any questions

Papers and Posters

  • Paper about BMTK’s BioNet simulator can be found on PLOS ONE

SONATA Data Format

The SONATA data format was developed jointly by the Allen Institute and the Blue Brain Project as a standarized, cross-platform format for storing large scale networks and simulation results. The BMTK utilizes when building and simulating networks. Not only does this improve performance and file size, but it lets the BMTK interact with the growing list of software that supports the SONATA format.

More information about the SONATA (and hence BMTK) data format can be found at the SONATA github page

Acknowledgements

We wish to thank the Allen Institute for Brain Science Founders, Paul G. Allen and Jody Allen, for their vision, encouragement, and support.