Literature DB >> 35074827

NDI: A Platform-Independent Data Interface and Database for Neuroscience Physiology and Imaging Experiments.

Daniel García Murillo1,2,3, Yixin Zhao3, Ora S Rogovin2, Kelly Zhang1,3, Andrew W Hu1, Mo Re Kim1, Shufei Chen2,3, Ziqi Wang1,3, Zoey C Keeley2, Daniel I Shin2, Victor M Suárez Casanova2, Yannan Zhu2, Lisandro Martin2, Olga Papaemmanouil4,3, Stephen D Van Hooser5,2,4,6.   

Abstract

Collaboration in neuroscience is impeded by the difficulty of sharing primary data, results, and software across labs. Here, we introduce Neuroscience Data Interface (NDI), a platform-independent standard that allows an analyst to use and create software that functions independently from the format of the raw data or the manner in which the data are organized into files. The interface is rooted in a simple vocabulary that describes common apparatus and storage devices used in neuroscience experiments. Results of analyses, and analyses of analyses, are stored as documents in a scalable, queryable database that stores the relationships and history among the experiment elements and documents. The interface allows the development of an application ecosystem where applications can focus on calculation rather than data format or organization. This tool can be used by individual labs to exchange and analyze data, and it can serve to curate neuroscience data for searchable archives.
Copyright © 2022 García Murillo et al.

Entities:  

Keywords:  BRAIN initiative; brain science; data acquisition; data archive; queries

Mesh:

Year:  2022        PMID: 35074827      PMCID: PMC8874953          DOI: 10.1523/ENEURO.0073-21.2022

Source DB:  PubMed          Journal:  eNeuro        ISSN: 2373-2822


  26 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.  Impact of precisely-timed inhibition of gustatory cortex on taste behavior depends on single-trial ensemble dynamics.

Authors:  Narendra Mukherjee; Joseph Wachutka; Donald B Katz
Journal:  Elife       Date:  2019-06-24       Impact factor: 8.140

3.  Data sharing for computational neuroscience.

Authors:  Jeffrey L Teeters; Kenneth D Harris; K Jarrod Millman; Bruno A Olshausen; Friedrich T Sommer
Journal:  Neuroinformatics       Date:  2008-02-08

4.  OpenfMRI: Open sharing of task fMRI data.

Authors:  Russell A Poldrack; Krzysztof J Gorgolewski
Journal:  Neuroimage       Date:  2015-06-03       Impact factor: 6.556

5.  BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods.

Authors:  Krzysztof J Gorgolewski; Fidel Alfaro-Almagro; Tibor Auer; Pierre Bellec; Mihai Capotă; M Mallar Chakravarty; Nathan W Churchill; Alexander Li Cohen; R Cameron Craddock; Gabriel A Devenyi; Anders Eklund; Oscar Esteban; Guillaume Flandin; Satrajit S Ghosh; J Swaroop Guntupalli; Mark Jenkinson; Anisha Keshavan; Gregory Kiar; Franziskus Liem; Pradeep Reddy Raamana; David Raffelt; Christopher J Steele; Pierre-Olivier Quirion; Robert E Smith; Stephen C Strother; Gaël Varoquaux; Yida Wang; Tal Yarkoni; Russell A Poldrack
Journal:  PLoS Comput Biol       Date:  2017-03-09       Impact factor: 4.475

Review 6.  Best practices in data analysis and sharing in neuroimaging using MRI.

Authors:  Thomas E Nichols; Samir Das; Simon B Eickhoff; Alan C Evans; Tristan Glatard; Michael Hanke; Nikolaus Kriegeskorte; Michael P Milham; Russell A Poldrack; Jean-Baptiste Poline; Erika Proal; Bertrand Thirion; David C Van Essen; Tonya White; B T Thomas Yeo
Journal:  Nat Neurosci       Date:  2017-02-23       Impact factor: 24.884

7.  odMLtables: A User-Friendly Approach for Managing Metadata of Neurophysiological Experiments.

Authors:  Julia Sprenger; Lyuba Zehl; Jana Pick; Michael Sonntag; Jan Grewe; Thomas Wachtler; Sonja Grün; Michael Denker
Journal:  Front Neuroinform       Date:  2019-09-27       Impact factor: 4.081

8.  Synaptic and intrinsic mechanisms underlying development of cortical direction selectivity.

Authors:  Arani Roy; Jason J Osik; Benyamin Meschede-Krasa; Wesley T Alford; Daniel P Leman; Stephen D Van Hooser
Journal:  Elife       Date:  2020-07-23       Impact factor: 8.140

9.  QUANTITATIVE REEVALUATION OF THE EFFECTS OF SHORT- AND LONG-TERM REMOVAL OF DESCENDING MODULATORY INPUTS ON THE PYLORIC RHYTHM OF THE CRAB, CANCER BOREALIS.

Authors:  Albert W Hamood; Sara A Haddad; Adriane G Otopalik; Philipp Rosenbaum; Eve Marder
Journal:  eNeuro       Date:  2015-01

10.  SpikeInterface, a unified framework for spike sorting.

Authors:  Alessio P Buccino; Cole L Hurwitz; Samuel Garcia; Jeremy Magland; Joshua H Siegle; Roger Hurwitz; Matthias H Hennig
Journal:  Elife       Date:  2020-11-10       Impact factor: 8.140

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