Connectivity concepts in neuronal network modeling

PLoS Computational Biology, vol. 18, pp. e1010086

Abstract

Sustainable research on computational models of neuronal networks requires published models to be understandable, reproducible, and extendable. Missing details or ambiguities about mathematical concepts and assumptions, algorithmic implementations, or parameterizations hinder progress. Such flaws are unfortunately frequent and one reason is a lack of readily applicable standards and tools for model description. Our work aims to advance complete and concise descriptions of network connectivity but also to guide the implementation of connection routines in simulation software and neuromorphic hardware systems. We first review models made available by the computational neuroscience community in the repositories ModelDB and Open Source Brain, and investigate the corresponding connectivity structures and their descriptions in both manuscript and code. The review comprises the connectivity of networks with diverse levels of neuroanatomical detail and exposes how connectivity is abstracted in existing description languages and simulator interfaces. We find that a substantial proportion of the published descriptions of connectivity is ambiguous. Based on this review, we derive a set of connectivity concepts for deterministically and probabilistically connected networks and also address networks embedded in metric space. Beside these mathematical and textual guidelines, we propose a unified graphical notation for network diagrams to facilitate an intuitive understanding of network properties. Examples of representative network models demonstrate the practical use of the ideas. We hope that the proposed standardizations will contribute to unambiguous descriptions and reproducible implementations of neuronal network connectivity in computational neuroscience.

Authors 10

1. Johanna Senk corresponding

   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-Institut Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany

2. Birgit Kriener corresponding

   University of Oslo

   Affiliation as printed

   Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway

3. Mikael Djurfeldt corresponding

   KTH Royal Institute of Technology

   Affiliation as printed

   PDC Center for High-Performance Computing, KTH Royal Institute of Technology, Stockholm, Sweden

4. Nicole Voges corresponding

   Aix-Marseille Université · Institut de Neurosciences de la Timone

   Affiliation as printed

   INT UMR 7289, Aix-Marseille University, Marseille, France

5. Han-Jia Jiang corresponding

   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-Institut Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany

   Institute of Zoology, University of Cologne, Cologne, Germany

6. Lisa Schüttler corresponding Aachen Chair of Theory of Science and Technology Human Technology Center

   RWTH Aachen University

   Affiliation as printed

   Chair of Theory of Science and Technology, Human Technology Center, RWTH Aachen University, Aachen, Germany

7. Gabriele Gramelsberger corresponding Aachen Chair of Theory of Science and Technology Human Technology Center

   RWTH Aachen University

   Affiliation as printed

   Chair of Theory of Science and Technology, Human Technology Center, RWTH Aachen University, Aachen, Germany

8. Markus Diesmann corresponding Aachen Department of Physics Faculty 1 Department of Psychiatry, Psychotherapy and Psychosomatics School of Medicine

   Forschungszentrum Jülich · Jülich Aachen Research Alliance · RWTH Aachen University

   Affiliation as printed

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

   Department of Psychiatry, Psychotherapy and Psychosomatics, School of Medicine, RWTH Aachen University, Aachen, Germany

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

9. Hans Ekkehard Pleßer corresponding

   Forschungszentrum Jülich · Jülich Aachen Research Alliance · Norwegian University of Life Sciences

   Affiliation as printed

   Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway

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

10. Sacha Jennifer van Albada corresponding

    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-Institut Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany

    Institute of Zoology, University of Cologne, Cologne, Germany