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Linking Scientific Instruments and Computation: Patterns, Technologies, and Experiences

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Journal Patterns (N Y)
Date 2022 Oct 24
PMID 36277824
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Abstract

Powerful detectors at modern experimental facilities routinely collect data at multiple GB/s. Online analysis methods are needed to enable the collection of only interesting subsets of such massive data streams, such as by explicitly discarding some data elements or by directing instruments to relevant areas of experimental space. Thus, methods are required for configuring and running distributed computing pipelines-what we call flows-that link instruments, computers (e.g., for analysis, simulation, artificial intelligence [AI] model training), edge computing (e.g., for analysis), data stores, metadata catalogs, and high-speed networks. We review common patterns associated with such flows and describe methods for instantiating these patterns. We present experiences with the application of these methods to the processing of data from five different scientific instruments, each of which engages powerful computers for data inversion,model training, or other purposes. We also discuss implications of such methods for operators and users of scientific facilities.

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References
1.
Deng J, Preissner C, Klug J, Mashrafi S, Roehrig C, Jiang Y . The Velociprobe: An ultrafast hard X-ray nanoprobe for high-resolution ptychographic imaging. Rev Sci Instrum. 2019; 90(8):083701. DOI: 10.1063/1.5103173. View

2.
Maiden A, Humphry M, Zhang F, Rodenburg J . Superresolution imaging via ptychography. J Opt Soc Am A Opt Image Sci Vis. 2011; 28(4):604-12. DOI: 10.1364/JOSAA.28.000604. View

3.
Cherukara M, Nashed Y, Harder R . Real-time coherent diffraction inversion using deep generative networks. Sci Rep. 2018; 8(1):16520. PMC: 6224523. DOI: 10.1038/s41598-018-34525-1. View

4.
Goecks J, Nekrutenko A, Taylor J . Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 2010; 11(8):R86. PMC: 2945788. DOI: 10.1186/gb-2010-11-8-r86. View

5.
Benecke G, Wagermaier W, Li C, Schwartzkopf M, Flucke G, Hoerth R . A customizable software for fast reduction and analysis of large X-ray scattering data sets: applications of the new package to small-angle X-ray scattering and grazing-incidence small-angle X-ray scattering. J Appl Crystallogr. 2014; 47(Pt 5):1797-1803. PMC: 4180741. DOI: 10.1107/S1600576714019773. View