Literature DB >> 36193886

The Neurodata Without Borders ecosystem for neurophysiological data science.

Oliver Rübel1, Andrew Tritt2, Ryan Ly1, Benjamin K Dichter3, Satrajit Ghosh4,5, Lawrence Niu6, Pamela Baker7, Ivan Soltesz8, Lydia Ng7, Karel Svoboda7,9, Loren Frank9,10,11, Kristofer E Bouchard1,10,12,13,14.   

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.
© 2022, Rübel, Tritt, Ly et al.

Entities:  

Keywords:  FAIR data; Neurophysiology; archive; data ecosystem; data language; data standard; human; mouse; neuroscience; rat

Mesh:

Year:  2022        PMID: 36193886      PMCID: PMC9531949          DOI: 10.7554/eLife.78362

Source DB:  PubMed          Journal:  Elife        ISSN: 2050-084X            Impact factor:   8.713


  27 in total

1.  Neurodata Without Borders: Creating a Common Data Format for Neurophysiology.

Authors:  Jeffery L Teeters; Keith Godfrey; Rob Young; Chinh Dang; Claudia Friedsam; Barry Wark; Hiroki Asari; Simon Peron; Nuo Li; Adrien Peyrache; Gennady Denisov; Joshua H Siegle; Shawn R Olsen; Christopher Martin; Miyoung Chun; Shreejoy Tripathy; Timothy J Blanche; Kenneth Harris; György Buzsáki; Christof Koch; Markus Meister; Karel Svoboda; Friedrich T Sommer
Journal:  Neuron       Date:  2015-11-18       Impact factor: 17.173

2.  The broken promise that undermines human genome research.

Authors:  Kendall Powell
Journal:  Nature       Date:  2021-02       Impact factor: 49.962

3.  Open Ephys: an open-source, plugin-based platform for multichannel electrophysiology.

Authors:  Joshua H Siegle; Aarón Cuevas López; Yogi A Patel; Kirill Abramov; Shay Ohayon; Jakob Voigts
Journal:  J Neural Eng       Date:  2017-08       Impact factor: 5.379

4.  Interneuronal mechanisms of hippocampal theta oscillations in a full-scale model of the rodent CA1 circuit.

Authors:  Marianne J Bezaire; Ivan Raikov; Kelly Burk; Dhrumil Vyas; Ivan Soltesz
Journal:  Elife       Date:  2016-12-23       Impact factor: 8.140

5.  High-Performance Computing in Neuroscience for Data-Driven Discovery, Integration, and Dissemination.

Authors:  Kristofer E Bouchard; James B Aimone; Miyoung Chun; Thomas Dean; Michael Denker; Markus Diesmann; David D Donofrio; Loren M Frank; Narayanan Kasthuri; Chirstof Koch; Oliver Ruebel; Horst D Simon; Friedrich T Sommer
Journal:  Neuron       Date:  2016-11-02       Impact factor: 17.173

6.  CaImAn an open source tool for scalable calcium imaging data analysis.

Authors:  Andrea Giovannucci; Johannes Friedrich; Pat Gunn; Jérémie Kalfon; Brandon L Brown; Sue Ann Koay; Jiannis Taxidis; Farzaneh Najafi; Jeffrey L Gauthier; Pengcheng Zhou; Baljit S Khakh; David W Tank; Dmitri B Chklovskii; Eftychios A Pnevmatikakis
Journal:  Elife       Date:  2019-01-17       Impact factor: 8.140

7.  AJILE12: Long-term naturalistic human intracranial neural recordings and pose.

Authors:  Steven M Peterson; Satpreet H Singh; Benjamin Dichter; Michael Scheid; Rajesh P N Rao; Bingni W Brunton
Journal:  Sci Data       Date:  2022-04-21       Impact factor: 8.501

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

Authors:  Padraig Gleeson; Matteo Cantarelli; Boris Marin; Adrian Quintana; Matt Earnshaw; Sadra Sadeh; Eugenio Piasini; Justas Birgiolas; Robert C Cannon; N Alex Cayco-Gajic; Sharon Crook; Andrew P Davison; Salvador Dura-Bernal; András Ecker; Michael L Hines; Giovanni Idili; Frederic Lanore; Stephen D Larson; William W Lytton; Amitava Majumdar; Robert A McDougal; Subhashini Sivagnanam; Sergio Solinas; Rokas Stanislovas; Sacha J van Albada; Werner van Geit; R Angus Silver
Journal:  Neuron       Date:  2019-06-11       Impact factor: 17.173

9.  RAVE: Comprehensive open-source software for reproducible analysis and visualization of intracranial EEG data.

Authors:  John F Magnotti; Zhengjia Wang; Michael S Beauchamp
Journal:  Neuroimage       Date:  2020-09-10       Impact factor: 6.556

10.  Relationship between simultaneously recorded spiking activity and fluorescence signal in GCaMP6 transgenic mice.

Authors:  Lawrence Huang; Peter Ledochowitsch; Ulf Knoblich; Jérôme Lecoq; Gabe J Murphy; R Clay Reid; Saskia Ej de Vries; Christof Koch; Hongkui Zeng; Michael A Buice; Jack Waters; Lu Li
Journal:  Elife       Date:  2021-03-08       Impact factor: 8.140

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  1 in total

1.  Is Neuroscience FAIR? A Call for Collaborative Standardisation of Neuroscience Data.

Authors:  Jean-Baptiste Poline; David N Kennedy; Friedrich T Sommer; Giorgio A Ascoli; David C Van Essen; Adam R Ferguson; Jeffrey S Grethe; Michael J Hawrylycz; Paul M Thompson; Russell A Poldrack; Satrajit S Ghosh; David B Keator; Thomas L Athey; Joshua T Vogelstein; Helen S Mayberg; Maryann E Martone
Journal:  Neuroinformatics       Date:  2022-01-21
  1 in total

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