NEST Desktop - An educational application for neuroscience

bioRxiv (Cold Spring Harbor Laboratory)

Abstract

Abstract Simulation software for spiking neuronal network models matured in the past decades regarding performance and flexibility. But the entry barrier remains high for students and early career scientists in computational neuroscience since these simulators typically require programming skills and a complex installation. Here, we describe an installation-free Graphical User Interface (GUI) running in the web browser, which is distinct from the simulation engine running anywhere, on the student’s laptop or on a supercomputer. This architecture provides robustness against technological changes in the software stack and simplifies deployment for self-education and for teachers. Our new open source tool, NEST Desktop, comprises graphical elements for creating and configuring network models, running simulations, and visualizing and analyzing the results. NEST Desktop allows students to explore important concepts in computational neuroscience without the need to learn a simulator control language before. Our experiences so far highlight that NEST Desktop helps advancing both quality and intensity of teaching in computational neuroscience in regular university courses. We view the availability of the tool on public resources like the European ICT infrastructure for neuroscience EBRAINS as a contribution to equal opportunities. Significance Statement The graphical user interface NEST Desktop makes neuronal network simulations accessible to non-programmers. It facilitates the interactive exploration of neuronal network models by integrating the whole workflow of wiring up the setup, simulating the neuronal dynamics, and analyzing the recorded activity data into a single tool. NEST Desktop effectively supports teaching the concepts and methods of computational neuroscience. Due to its installation-free web-based implementation, it is in particularly suitable for online courses.

Authors 5

1. Sebastian Spreizer corresponding

   University of Freiburg · Forschungszentrum Jülich · Bernstein Center for Computational Neuroscience Freiburg · Jülich Aachen Research Alliance · Universität Trier

   Affiliation as printed

   Bernstein Center Freiburg, University of Freiburg, 79104 Freiburg, Germany

   Department of Computer Science, University of Trier, 54296 Trier, Germany

   Faculty of Biology, University of Freiburg, 79104 Freiburg, 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, 52428 Jülich, Germany

   Department of Computer Science, University of Trier, 5296 Trier, 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, 52428 Jülich, Germany

3. Stefan Rotter

   University of Freiburg · Bernstein Center for Computational Neuroscience Freiburg

   Affiliation as printed

   Bernstein Center Freiburg, University of Freiburg, 79104 Freiburg, Germany

   Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany

   Faculty of Biology, University of Freiburg, 7904 Freiburg, Germany

4. Markus Diesmann 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, 52074 Aachen, Germany

   Department of Psychiatry, Psychotherapy and Psychosomatics, School of Medicine, RWTH Aachen University, 52074 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, 52428 Jülich, Germany

   Department of Psychiatry, Psychotherapy and Psychosomatics, School of Medicine, RWTH Aachen University, 2074 Aachen, Germany

5. Benjamin Weyers

   Universität Trier

   Affiliation as printed

   Department of Computer Science, University of Trier, 54296 Trier, Germany

   Department of Computer Science, University of Trier, 5296 Trier, Germany