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


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.

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.

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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:07 Faculty of Science > Institute of Neuroinformatics
Dewey Decimal Classification:570 Life sciences; biology
Language:English
Date:1 August 2019
Deposited On:13 Feb 2020 10:09
Last Modified:13 Feb 2020 10:09
Publisher:Cell Press (Elsevier)
ISSN:0896-6273
OA Status:Green
Free access at:Publisher DOI. An embargo period may apply.
Publisher DOI:https://doi.org/10.1016/j.neuron.2019.05.019
Project Information:
  • : FunderSNSF
  • : Grant IDPA0033-101445
  • : Project TitleAnalysis of the functional environment and the mechanism of action of the putative AAA-type ATPase Rix7p during ribosome biogenesis in Saccharomyces cerevisiae
  • : FunderFP7
  • : Grant ID294667
  • : Project TitleNEUROGAIN - Nonlinear synaptic integration in morphologically simple and complex neurons
  • : FunderFP7
  • : Grant ID238686
  • : Project TitleCEREBNET - Timing and plasticity in the olivo-cerebellar system
  • : FunderFP7
  • : Grant ID604102
  • : Project TitleHBP - The Human Brain Project
  • : FunderH2020
  • : Grant ID720270
  • : Project TitleHBP SGA1 - Human Brain Project Specific Grant Agreement 1

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