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The Neurodata Without Borders ecosystem for neurophysiological data science

View ORCID ProfileOliver Rübel, Andrew Tritt, Ryan Ly, View ORCID ProfileBenjamin K. Dichter, View ORCID ProfileSatrajit Ghosh, Lawrence Niu, Ivan Soltesz, Karel Svoboda, Loren Frank, Kristofer E. Bouchard
doi: https://doi.org/10.1101/2021.03.13.435173
Oliver Rübel
1Scientific Data Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Andrew Tritt
2Applied Mathematics and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Ryan Ly
1Scientific Data Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Benjamin K. Dichter
3CatalystNeuro, Benicia, CA, USA
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Satrajit Ghosh
4McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
5Department of Otolaryngology - Head and Neck Surgery, Harvard Medical School, Boston, MA, USA
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Lawrence Niu
6MBF Bioscience, Ashburn, VA
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Ivan Soltesz
7Department of Neurosurgery, Stanford University, Stanford, CA, USA,
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Karel Svoboda
8Allen Institute for Brain Science, Seattle, WA, USA
9Howard Hughes Medical Institute
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Loren Frank
9Howard Hughes Medical Institute
10Kavli Institute for Fundamental Neuroscience, San Francisco, CA, USA
11Departments of Physiology and Psychiatry University of California, San Francisco, CA, USA
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Kristofer E. Bouchard
1Scientific Data Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
10Kavli Institute for Fundamental Neuroscience, San Francisco, CA, USA
12Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
13Helen Wills Neuroscience Institute and Redwood Center for Theoretical Neuroscience, University of California, Berkeley, CA, USA
14Weill Neurohub
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  • For correspondence: kebouchard@lbl.gov
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Abstract

The neurophysiology of cells and tissues are monitored electrophysiologically and optically in diverse experiments and species, ranging from flies to humans. Understanding the brain requires integration of data across this diversity, and thus these data must be findable, accessible, interoperable, and reusable (FAIR). This requires a standard language for data and metadata that can coevolve with neuroscience. We describe design and implementation principles for a language for neurophysiology data. Our open-source software (Neurodata Without Borders, NWB) defines and modularizes the interdependent, yet separable, components of a data language. We demonstrate NWB’s impact through unified description of neurophysiology data across diverse modalities and species. NWB exists in an ecosystem, which includes data management, analysis, visualization, and archive tools. Thus, the NWB data language enables reproduction, interchange, and reuse of diverse neurophysiology data. More broadly, the design principles of NWB are generally applicable to enhance discovery across biology through data FAIRness.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • ↵* equal contributors;

  • ↵$ contact authors

  • The authors have updated the manuscript to: 1) provide more technical details and clarifying the conceptual and technical innovations relative to previous technologies and how these innovations enable researchers to share data in compliance with FAIR principles with the community and foster collaboration, 2) provide more details on examples demonstrating the utility of NWB to harmoniously store diverse neurophysiology data types 3) discuss more clearly the short-term advantages for individual researchers, especially those generating data, of adopting NWB towards broader adoption 4) clarify text and language where appropriate

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted March 29, 2022.
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The Neurodata Without Borders ecosystem for neurophysiological data science
Oliver Rübel, Andrew Tritt, Ryan Ly, Benjamin K. Dichter, Satrajit Ghosh, Lawrence Niu, Ivan Soltesz, Karel Svoboda, Loren Frank, Kristofer E. Bouchard
bioRxiv 2021.03.13.435173; doi: https://doi.org/10.1101/2021.03.13.435173
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The Neurodata Without Borders ecosystem for neurophysiological data science
Oliver Rübel, Andrew Tritt, Ryan Ly, Benjamin K. Dichter, Satrajit Ghosh, Lawrence Niu, Ivan Soltesz, Karel Svoboda, Loren Frank, Kristofer E. Bouchard
bioRxiv 2021.03.13.435173; doi: https://doi.org/10.1101/2021.03.13.435173

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