NNMT: Mean-Field Based Analysis Tools for Neuronal Network Models

Frontiers in Neuroinformatics, vol. 16, pp. 835657

Abstract

Mean-field theory of neuronal networks has led to numerous advances in our analytical and intuitive understanding of their dynamics during the past decades. In order to make mean-field based analysis tools more accessible, we implemented an extensible, easy-to-use open-source Python toolbox that collects a variety of mean-field methods for the leaky integrate-and-fire neuron model. The Neuronal Network Mean-field Toolbox (NNMT) in its current state allows for estimating properties of large neuronal networks, such as firing rates, power spectra, and dynamical stability in mean-field and linear response approximation, without running simulations. In this article, we describe how the toolbox is implemented, show how it is used to reproduce results of previous studies, and discuss different use-cases, such as parameter space explorations, or mapping different network models. Although the initial version of the toolbox focuses on methods for leaky integrate-and-fire neurons, its structure is designed to be open and extensible. It aims to provide a platform for collecting analytical methods for neuronal network model analysis, such that the neuroscientific community can take maximal advantage of them.

Authors 6

1. Moritz Layer corresponding Aachen

   Forschungszentrum Jülich · Jülich Aachen Research Alliance · RWTH Aachen University

   Affiliation as printed

   Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany

   RWTH Aachen University, Aachen, Germany

2. Johanna Senk

   Forschungszentrum Jülich · Jülich Aachen Research Alliance

   Affiliation as printed

   Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany

3. Simon Essink Aachen

   Forschungszentrum Jülich · Jülich Aachen Research Alliance · RWTH Aachen University

   Affiliation as printed

   Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany

   RWTH Aachen University, Aachen, Germany

4. Alexander van Meegen

   Forschungszentrum Jülich · University of Cologne · Jülich Aachen Research Alliance

   Affiliation as printed

   Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany

   Institute of Zoology, Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, Germany

5. Hannah Bos

   Forschungszentrum Jülich · Jülich Aachen Research Alliance

   Affiliation as printed

   Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany

6. Moritz Helias Aachen Department of Physics Faculty 1

   Forschungszentrum Jülich · Jülich Aachen Research Alliance · RWTH Aachen University

   Affiliation as printed

   Department of Physics, Faculty 1, RWTH Aachen University, Aachen, Germany

   Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany