A mean-field toolbox for spiking neuronal network model analysis

bioRxiv (Cold Spring Harbor Laboratory)

Abstract

ABSTRACT Mean-field theory of spiking neuronal networks has led to numerous advances in our analytical and intuitive understanding of the dynamics of neuronal network models during the past decades. But, the elaborate nature of many of the developed methods, as well as the difficulty of implementing them, may limit the wider neuroscientific community from taking maximal advantage of these tools. In order to make them more accessible, we implemented an extensible, easy-to-use open-source Python toolbox that collects a variety of mean-field methods for the widely used 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 on high performance systems. In this article we describe how the toolbox is implemented, show how it is used to calculate neuronal network properties, and discuss different use-cases, such as extraction of network mechanisms, parameter space exploration, or hybrid modeling approaches. Although the initial version of the toolbox focuses on methods that are close to our own past and present research, its structure is designed to be open and extensible. It aims to provide a platform for collecting analytical methods for neuronal network model analysis and we discuss how interested scientists can share their own methods via this platform.

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

   Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA Institute Brain Structure-Function Relationships (INM-0), Jülich Research Centre, Jülich, 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

   Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA Institute Brain Structure-Function Relationships (INM-0), 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

   Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA Institute Brain Structure-Function Relationships (INM-0), Jülich Research Centre, Jülich, 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

   Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA Institute Brain Structure-Function Relationships (INM-0), Jülich Research Centre, Jülich, 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

   Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA Institute Brain Structure-Function Relationships (INM-0), 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

   Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA Institute Brain Structure-Function Relationships (INM-0), Jülich Research Centre, Jülich, Germany