Brain Modeling ToolKit: An open source software suite for multiscale modeling of brain circuits
Fig 2
Basic workflow that is conserved across modules of BMTK.
Input SONATA files (represented symbolically as chests of drawers) determine the composition and properties of the nodes/network, as well as incoming stimuli (spikes, firing rates, movies) and simulation configuration. Top: the model construction stage. The BMTK Builder combines elements such as cell or synapse models, connectivity rules, and others, via high-level specifications, instantiates the network model, and saves the instantiation as a set of SONATA files. Bottom: simulation stage. The BMTK simulator modules take in the SONATA files as inputs and perform simulations. The input SONATA files may be generated by the BMTK Builder (dashed arrow), any other Builder software supporting SONATA, or from public repositories, collaborators, etc. The BMTK simulator modules produce output, also in SONATA format, typically containing spikes and/or time series (e.g., membrane voltage in selected cells, as a function of time). Right: the SONATA files produced by the BMTK Builder or simulator modules can be analyzed in terms of the model structure or simulated activity (using any analysis software supporting SONATA, or the software that can read HDF5, CSV, and other components of SONATA specification).