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intern: Integrated Toolkit for Extensible and Reproducible Neuroscience

View ORCID ProfileJordan Matelsky, Luis Rodriguez, Daniel Xenes, Timothy Gion, Robert Hider Jr., View ORCID ProfileBrock Wester, William Gray-Roncal
doi: https://doi.org/10.1101/2020.05.15.098707
Jordan Matelsky
Johns Hopkins University Applied Physics Laboratory; Laurel, Maryland
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Luis Rodriguez
Johns Hopkins University Applied Physics Laboratory; Laurel, Maryland
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Daniel Xenes
Johns Hopkins University Applied Physics Laboratory; Laurel, Maryland
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Timothy Gion
Johns Hopkins University Applied Physics Laboratory; Laurel, Maryland
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Robert Hider Jr.
Johns Hopkins University Applied Physics Laboratory; Laurel, Maryland
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Brock Wester
Johns Hopkins University Applied Physics Laboratory; Laurel, Maryland
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William Gray-Roncal
Johns Hopkins University Applied Physics Laboratory; Laurel, Maryland
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  • For correspondence: william.gray.roncal@jhuapl.edu
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Abstract

As neuroscience datasets continue to grow in size, the complexity of data analyses can require a detailed understanding and implementation of systems computer science for storage, access, processing, and sharing. Currently, several general data standards (e.g., Zarr, HDF5, precompute, tensorstore) and purpose-built ecosystems (e.g., BossDB, CloudVolume, DVID, and Knossos) exist. Each of these systems has advantages and limitations and is most appropriate for different use cases. Using datasets that don’t fit into RAM in this heterogeneous environment is challenging, and significant barriers exist to leverage underlying research investments. In this manuscript, we outline our perspective for how to approach this challenge through the use of community provided, standardized interfaces that unify various computational backends and abstract computer science challenges from the scientist. We introduce desirable design patterns and our reference implementation called intern.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://bossdb.org/tools/intern

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted May 16, 2020.
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intern: Integrated Toolkit for Extensible and Reproducible Neuroscience
Jordan Matelsky, Luis Rodriguez, Daniel Xenes, Timothy Gion, Robert Hider Jr., Brock Wester, William Gray-Roncal
bioRxiv 2020.05.15.098707; doi: https://doi.org/10.1101/2020.05.15.098707
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intern: Integrated Toolkit for Extensible and Reproducible Neuroscience
Jordan Matelsky, Luis Rodriguez, Daniel Xenes, Timothy Gion, Robert Hider Jr., Brock Wester, William Gray-Roncal
bioRxiv 2020.05.15.098707; doi: https://doi.org/10.1101/2020.05.15.098707

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