User Guide#

Overview of BMTK Workflow and Architecture#

The Brain Modeling Toolkit (BMTK) is a python-based software package for building, simulating and analyzing large-scale neural network models. It supports the building and simulation of models of varying levels-of-resolution; from multi-compartment biophysically detailed networks, to point-neuron models, to filter-based models, and even population-level firing rate models.

The BMTK is not itself a simulator and will utilize existing simulators, like NEURON and NEST, to run different types of models. What BMTK does provide:

The BMTK Workflow and architecture#

BMTK can readily scale to run models of single neurons, and even single compartments, and for all different types of neuronal networks. However BMTK was designed for very-large, highly optimized mammalian cortical network models. Generating the connectivity matrix could take hours or even days to complete. Plus once we had the base-line model we wanted to run against a large variety of conditions and stimuli, so that we could directly compare with existing in-vivo recordings (see Allen Brain Observatory).

Unlike other simulators, BMTK separates the process of building, simulating, and analyzing the results. First a fully instantiated base-line version of the model is built and saved to a file so each time a simulation is ran it takes only a small fraction of the time to instantiate the simulation. Results are also automatically saved to a disk. BMTK and the format it uses (SONATA, see below) makes it easy to dynamically adjust cell and synaptic parameters so that multiple iterations of a simulation be done as fast as possible

As such BMTK can be broken into three major components:

The Network Builder [bmtk.builder] - Used to build network models
The Simulation Engines [bmtk.simulator] - Interfaces for simulating the network
Analysis and Visualization Tools [bmtk.analyzer] - Python functions for analyzing and visualizing the
network and simulation results

The components can be as one workflow or separately by themselves. BMTK utilizes the SONATA Data format (see next section) to allow sharing of large-scale network data. As such, it is possible to use the Network Builder to build the model but another tool to run the model. Or if another model has been built by someone else and saved in SONATA format BMTK will be able to simulate it.