PyRates - a Python framework for rate-based neural simulations

Gast, Richard; Rose, Daniel; Salomon, Christoph; Möller, Harald E.; Weiskopf, Nikolaus; Knösche, Thomas R.

In neuroscience, computational modeling has become an important source of insight into brain states and dynamics. A basic requirement for computational modeling studies is the availability of efficient software for setting up models and performing numerical simulations. While many such tools exist for different families of neural models, there is a lack of tools allowing for both a generic model definition and efficiently parallelized simulations. In this work, we present PyRates, a Python framework that provides the means to build a large variety of rate-based neural models. PyRates provides intuitive access to and modification of all mathematical operators in a graph, thus allowing for a highly generic model definition. For computational efficiency and parallelization, the model is translated into a compute graph. Using the example of two different neural models belonging to the family of ratebased population models, we explain the mathematical formalism, software structure and user interfaces of PyRates. We show via numerical simulations that the behavior of the PyRates model implementations is consistent with the literature. Finally, we demonstrate the computational capacities and scalability of PyRates via a number of benchmark simulations of neural networks differing in size and connectivity.

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PyRates - a Python framework for rate-based neural simulations, 2019. . PLOS ONE / Public Library of Science 14, 2019, art. e0225900. https://doi.org/10.1371/journal.pone.0225900
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