Literature DB >> 25233306

From cosmos to connectomes: the evolution of data-intensive science.

Randal Burns1, Joshua T Vogelstein2, Alexander S Szalay3.   

Abstract

The analysis of data requires computation: originally by hand and more recently by computers. Different models of computing are designed and optimized for different kinds of data. In data-intensive science, the scale and complexity of data exceeds the comfort zone of local data stores on scientific workstations. Thus, cloud computing emerges as the preeminent model, utilizing data centers and high-performance clusters, enabling remote users to access and query subsets of the data efficiently. We examine how data-intensive computational systems originally built for cosmology, the Sloan Digital Sky Survey (SDSS), are now being used in connectomics, at the Open Connectome Project. We list lessons learned and outline the top challenges we expect to face. Success in computational connectomics would drastically reduce the time between idea and discovery, as SDSS did in cosmology.
Copyright © 2014 Elsevier Inc. All rights reserved.

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Year:  2014        PMID: 25233306     DOI: 10.1016/j.neuron.2014.08.045

Source DB:  PubMed          Journal:  Neuron        ISSN: 0896-6273            Impact factor:   17.173


  7 in total

1.  Comprehensive optical and data management infrastructure for high-throughput light-sheet microscopy of whole mouse brains.

Authors:  M Caroline Müllenbroich; Ludovico Silvestri; Leonardo Onofri; Irene Costantini; Marcel Van't Hoff; Leonardo Sacconi; Giulio Iannello; Francesco S Pavone
Journal:  Neurophotonics       Date:  2015-06-29       Impact factor: 3.593

2.  Light-sheet imaging for systems neuroscience.

Authors:  Philipp J Keller; Misha B Ahrens; Jeremy Freeman
Journal:  Nat Methods       Date:  2015-01       Impact factor: 28.547

3.  Data-Rich Spatial Profiling of Cancer Tissue: Astronomy Informs Pathology.

Authors:  Alexander S Szalay; Janis M Taube
Journal:  Clin Cancer Res       Date:  2022-08-15       Impact factor: 13.801

Review 4.  Toward Community-Driven Big Open Brain Science: Open Big Data and Tools for Structure, Function, and Genetics.

Authors:  Adam S Charles; Benjamin Falk; Nicholas Turner; Talmo D Pereira; Daniel Tward; Benjamin D Pedigo; Jaewon Chung; Randal Burns; Satrajit S Ghosh; Justus M Kebschull; William Silversmith; Joshua T Vogelstein
Journal:  Annu Rev Neurosci       Date:  2020-04-13       Impact factor: 15.553

5.  A resource from 3D electron microscopy of hippocampal neuropil for user training and tool development.

Authors:  Kristen M Harris; Josef Spacek; Maria Elizabeth Bell; Patrick H Parker; Laurence F Lindsey; Alexander D Baden; Joshua T Vogelstein; Randal Burns
Journal:  Sci Data       Date:  2015-09-01       Impact factor: 6.444

6.  Q&A: Array tomography.

Authors:  Stephen J Smith
Journal:  BMC Biol       Date:  2018-09-06       Impact factor: 7.431

7.  A Single-Cell Level and Connectome-Derived Computational Model of the Drosophila Brain.

Authors:  Yu-Chi Huang; Cheng-Te Wang; Ta-Shun Su; Kuo-Wei Kao; Yen-Jen Lin; Chao-Chun Chuang; Ann-Shyn Chiang; Chung-Chuan Lo
Journal:  Front Neuroinform       Date:  2019-01-10       Impact factor: 4.081

  7 in total

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