Literature DB >> 35870448

Neuroscience Cloud Analysis As a Service: An open-source platform for scalable, reproducible data analysis.

Taiga Abe1, Ian Kinsella2, Shreya Saxena3, E Kelly Buchanan1, Joao Couto4, John Briggs5, Sian Lee Kitt6, Ryan Glassman6, John Zhou6, Liam Paninski7, John P Cunningham8.   

Abstract

A key aspect of neuroscience research is the development of powerful, general-purpose data analyses that process large datasets. Unfortunately, modern data analyses have a hidden dependence upon complex computing infrastructure (e.g., software and hardware), which acts as an unaddressed deterrent to analysis users. Although existing analyses are increasingly shared as open-source software, the infrastructure and knowledge needed to deploy these analyses efficiently still pose significant barriers to use. In this work, we develop Neuroscience Cloud Analysis As a Service (NeuroCAAS): a fully automated open-source analysis platform offering automatic infrastructure reproducibility for any data analysis. We show how NeuroCAAS supports the design of simpler, more powerful data analyses and that many popular data analysis tools offered through NeuroCAAS outperform counterparts on typical infrastructure. Pairing rigorous infrastructure management with cloud resources, NeuroCAAS dramatically accelerates the dissemination and use of new data analyses for neuroscientific discovery.
Copyright © 2022 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  cloud compute; data analysis; ensembling; infrastructure-as-code; markerless tracking; open source; widefield calcium imaging

Mesh:

Year:  2022        PMID: 35870448      PMCID: PMC9464703          DOI: 10.1016/j.neuron.2022.06.018

Source DB:  PubMed          Journal:  Neuron        ISSN: 0896-6273            Impact factor:   18.688


  48 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.  Mapping Sub-Second Structure in Mouse Behavior.

Authors:  Alexander B Wiltschko; Matthew J Johnson; Giuliano Iurilli; Ralph E Peterson; Jesse M Katon; Stan L Pashkovski; Victoria E Abraira; Ryan P Adams; Sandeep Robert Datta
Journal:  Neuron       Date:  2015-12-16       Impact factor: 17.173

3.  Computer science. Automating science.

Authors:  David Waltz; Bruce G Buchanan
Journal:  Science       Date:  2009-04-03       Impact factor: 47.728

4.  Gaussian-process factor analysis for low-dimensional single-trial analysis of neural population activity.

Authors:  Byron M Yu; John P Cunningham; Gopal Santhanam; Stephen I Ryu; Krishna V Shenoy; Maneesh Sahani
Journal:  J Neurophysiol       Date:  2009-04-08       Impact factor: 2.714

5.  Neuropixels 2.0: A miniaturized high-density probe for stable, long-term brain recordings.

Authors:  Nicholas A Steinmetz; Cagatay Aydin; Anna Lebedeva; Michael Okun; Marius Pachitariu; Marius Bauza; Maxime Beau; Jai Bhagat; Claudia Böhm; Martijn Broux; Susu Chen; Jennifer Colonell; Richard J Gardner; Bill Karsh; Fabian Kloosterman; Dimitar Kostadinov; Carolina Mora-Lopez; John O'Callaghan; Junchol Park; Jan Putzeys; Britton Sauerbrei; Rik J J van Daal; Abraham Z Vollan; Shiwei Wang; Marleen Welkenhuysen; Zhiwen Ye; Joshua T Dudman; Barundeb Dutta; Adam W Hantman; Kenneth D Harris; Albert K Lee; Edvard I Moser; John O'Keefe; Alfonso Renart; Karel Svoboda; Michael Häusser; Sebastian Haesler; Matteo Carandini; Timothy D Harris
Journal:  Science       Date:  2021-04-16       Impact factor: 47.728

6.  Neuroscience: Big brain, big data.

Authors:  Esther Landhuis
Journal:  Nature       Date:  2017-01-25       Impact factor: 49.962

7.  Snakemake--a scalable bioinformatics workflow engine.

Authors:  Johannes Köster; Sven Rahmann
Journal:  Bioinformatics       Date:  2012-08-20       Impact factor: 6.937

8.  DeepLabCut: markerless pose estimation of user-defined body parts with deep learning.

Authors:  Alexander Mathis; Pranav Mamidanna; Kevin M Cury; Taiga Abe; Venkatesh N Murthy; Mackenzie Weygandt Mathis; Matthias Bethge
Journal:  Nat Neurosci       Date:  2018-08-20       Impact factor: 24.884

9.  Single-trial neural dynamics are dominated by richly varied movements.

Authors:  Simon Musall; Matthew T Kaufman; Ashley L Juavinett; Steven Gluf; Anne K Churchland
Journal:  Nat Neurosci       Date:  2019-09-24       Impact factor: 24.884

10.  BARcode DEmixing through Non-negative Spatial Regression (BarDensr).

Authors:  Shuonan Chen; Jackson Loper; Xiaoyin Chen; Alex Vaughan; Anthony M Zador; Liam Paninski
Journal:  PLoS Comput Biol       Date:  2021-03-08       Impact factor: 4.779

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  1 in total

1.  Neuroscience data analysis in the cloud.

Authors:  Nina Vogt
Journal:  Nat Methods       Date:  2022-09       Impact factor: 47.990

  1 in total

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