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Open Source Brain: A Collaborative Resource for Visualizing, Analyzing, Simulating, and Developing Standardized Models of Neurons and Circuits.

Authors
  • Gleeson, Padraig1
  • Cantarelli, Matteo2
  • Marin, Boris3
  • Quintana, Adrian1
  • Earnshaw, Matt1
  • Sadeh, Sadra1
  • Piasini, Eugenio4
  • Birgiolas, Justas5
  • Cannon, Robert C6
  • Cayco-Gajic, N Alex1
  • Crook, Sharon7
  • Davison, Andrew P8
  • Dura-Bernal, Salvador9
  • Ecker, András10
  • Hines, Michael L11
  • Idili, Giovanni12
  • Lanore, Frederic1
  • Larson, Stephen D13
  • Lytton, William W9
  • Majumdar, Amitava14
  • And 7 more
  • 1 Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK.
  • 2 Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK; MetaCell Limited, Oxford, UK.
  • 3 Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK; Centro de Matemática, Computação e Cognição, Universidade Federal do ABC, Santo André, Brazil. , (Brazil)
  • 4 Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK; Computational Neuroscience Initiative and Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA, USA.
  • 5 School of Life Sciences, Arizona State University, Tempe, AZ, USA.
  • 6 Annotate Software Limited, Edinburgh, UK.
  • 7 School of Life Sciences, Arizona State University, Tempe, AZ, USA; School of Mathematical and Statistical Sciences, Arizona State University, Tempe, AZ, USA.
  • 8 Unité de Neuroscience, Information et Complexité, Centre National de la Recherche Scientifique, Paris, France. , (France)
  • 9 SUNY Downstate Medical Center and Kings County Hospital, Brooklyn, NY, USA.
  • 10 Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK; Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland. , (Switzerland)
  • 11 Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA.
  • 12 MetaCell Limited, Oxford, UK.
  • 13 OpenWorm Foundation, Boston, MA, USA.
  • 14 University of California, San Diego, San Diego, CA, USA.
  • 15 Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA; Center for Medical Informatics, Yale University, New Haven, CT, USA.
  • 16 Department of Biomedical Science, University of Sassari, Sassari, Italy; Institute of Neuroinformatics, University of Zurich and ETH Zurich, Zurich, Switzerland. , (Switzerland)
  • 17 Institute of Neuroscience and Medicine (INM-6), Institute for Advanced Simulation (IAS-6) and JARA-Institut Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany. , (Germany)
  • 18 Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland. , (Switzerland)
  • 19 Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK. Electronic address: [email protected]
Type
Published Article
Journal
Neuron
Publication Date
Aug 07, 2019
Volume
103
Issue
3
Identifiers
DOI: 10.1016/j.neuron.2019.05.019
PMID: 31201122
Source
Medline
Keywords
Language
English
License
Unknown

Abstract

Computational models are powerful tools for exploring the properties of complex biological systems. In neuroscience, data-driven models of neural circuits that span multiple scales are increasingly being used to understand brain function in health and disease. But their adoption and reuse has been limited by the specialist knowledge required to evaluate and use them. To address this, we have developed Open Source Brain, a platform for sharing, viewing, analyzing, and simulating standardized models from different brain regions and species. Model structure and parameters can be automatically visualized and their dynamical properties explored through browser-based simulations. Infrastructure and tools for collaborative interaction, development, and testing are also provided. We demonstrate how existing components can be reused by constructing new models of inhibition-stabilized cortical networks that match recent experimental results. These features of Open Source Brain improve the accessibility, transparency, and reproducibility of models and facilitate their reuse by the wider community. Copyright © 2019 The Authors. Published by Elsevier Inc. All rights reserved.

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