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A DNA-Based Archival Storage System

Authors:

James Bornholt,

Randolph Lopez,

Douglas M. Carmean,

Karin StraussAuthors Info & Claims

ASPLOS '16: Proceedings of the Twenty-First International Conference on Architectural Support for Programming Languages and Operating Systems

Pages 637 - 649

https://doi.org/10.1145/2872362.2872397

Published: 25 March 2016 Publication History

Abstract

Demand for data storage is growing exponentially, but the capacity of existing storage media is not keeping up. Using DNA to archive data is an attractive possibility because it is extremely dense, with a raw limit of 1 exabyte/mm³ (109 GB/mm³), and long-lasting, with observed half-life of over 500 years. This paper presents an architecture for a DNA-based archival storage system. It is structured as a key-value store, and leverages common biochemical techniques to provide random access. We also propose a new encoding scheme that offers controllable redundancy, trading off reliability for density. We demonstrate feasibility, random access, and robustness of the proposed encoding with wet lab experiments involving 151 kB of synthesized DNA and a 42 kB random-access subset, and simulation experiments of larger sets calibrated to the wet lab experiments. Finally, we highlight trends in biotechnology that indicate the impending practicality of DNA storage for much larger datasets.

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Cited By

Hong JRasool AWang SZiou DJiang Q(2024)VSD: A Novel Method for Video Segmentation and Storage in DNA Using RS CodeMathematics10.3390/math1208123512:8(1235)Online publication date: 19-Apr-2024
https://doi.org/10.3390/math12081235
Weide-Zaage K(2024)Dna Digital-storage: Advantages, Approach and Technical Implementation2024 Pan Pacific Strategic Electronics Symposium (Pan Pacific)10.23919/PanPacific60013.2024.10436508(1-6)Online publication date: 29-Jan-2024
https://doi.org/10.23919/PanPacific60013.2024.10436508
Leblanc JBoulle ORoux ENicolas JLavenier DAudic Y(2024) Fully in vitro iterative construction of a 24 kb-long artificial DNA sequence to store digital information BioTechniques10.2144/btn-2023-010976:5(207-219)Online publication date: 4-Jun-2024
https://doi.org/10.2144/btn-2023-0109
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Index Terms

A DNA-Based Archival Storage System
1. Hardware
  1. Emerging technologies
    1. Emerging interfaces
    2. Memory and dense storage
2. Information systems
  1. Information retrieval
    1. Specialized information retrieval
      1. Structure and multilingual text search
        Chemical and biochemical retrieval

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cover image ACM Conferences

ASPLOS '16: Proceedings of the Twenty-First International Conference on Architectural Support for Programming Languages and Operating Systems

March 2016

824 pages

ISBN:9781450340915

DOI:10.1145/2872362

General Chair:
Tom Conte
Georgia Tech, USA
,
Program Chair:
Yuanyuan Zhou
University of California, San Diego, USA

ACM SIGARCH Computer Architecture News Volume 44, Issue 2
ASPLOS'16
May 2016
774 pages
ISSN:0163-5964
DOI:10.1145/2980024
Editor:
Doug DeGroot
acm dot org
Issue’s Table of Contents
ACM SIGPLAN Notices Volume 51, Issue 4
ASPLOS '16
April 2016
774 pages
ISSN:0362-1340
EISSN:1558-1160
DOI:10.1145/2954679
Editor:
Andy Gill
University of Kansas, Lawrence, KS
Issue’s Table of Contents

Copyright © 2016 ACM.

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Published: 25 March 2016

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ASPLOS '16

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ASPLOS '16: Architectural Support for Programming Languages and Operating Systems

April 2 - 6, 2016

Georgia, Atlanta, USA

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ASPLOS '16 Paper Acceptance Rate 53 of 232 submissions, 23%;

Overall Acceptance Rate 535 of 2,713 submissions, 20%

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Cited By

Hong JRasool AWang SZiou DJiang Q(2024)VSD: A Novel Method for Video Segmentation and Storage in DNA Using RS CodeMathematics10.3390/math1208123512:8(1235)Online publication date: 19-Apr-2024
https://doi.org/10.3390/math12081235
Weide-Zaage K(2024)Dna Digital-storage: Advantages, Approach and Technical Implementation2024 Pan Pacific Strategic Electronics Symposium (Pan Pacific)10.23919/PanPacific60013.2024.10436508(1-6)Online publication date: 29-Jan-2024
https://doi.org/10.23919/PanPacific60013.2024.10436508
Leblanc JBoulle ORoux ENicolas JLavenier DAudic Y(2024) Fully in vitro iterative construction of a 24 kb-long artificial DNA sequence to store digital information BioTechniques10.2144/btn-2023-010976:5(207-219)Online publication date: 4-Jun-2024
https://doi.org/10.2144/btn-2023-0109
Wei YLi BDu DTsafrir DMusuvathi MGupta RAbu-Ghazaleh N(2024)An Encoding Scheme to Enlarge Practical DNA Storage Capacity by Reducing Primer-Payload CollisionsProceedings of the 29th ACM International Conference on Architectural Support for Programming Languages and Operating Systems, Volume 210.1145/3620665.3640417(71-84)Online publication date: 27-Apr-2024
https://dl.acm.org/doi/10.1145/3620665.3640417
Lin YLiang YChang YShih WLim WHong JPark J(2024)Bridging DNA Storage and Computation: An Integrated Framework for Efficient Biomolecular Data ManagementProceedings of the 39th ACM/SIGAPP Symposium on Applied Computing10.1145/3605098.3636017(196-203)Online publication date: 8-Apr-2024
https://dl.acm.org/doi/10.1145/3605098.3636017
Kim JJeong JKwak HNo J(2024)Design of DNA Storage Coding Scheme With LDPC Codes and InterleavingIEEE Transactions on NanoBioscience10.1109/TNB.2024.337997623:3(447-457)Online publication date: Jul-2024
https://doi.org/10.1109/TNB.2024.3379976
Jeong JPark HKwak HNo JJeon HLee JKim J(2024)Iterative Soft Decoding Algorithm for DNA Storage Using Quality Score and RedecodingIEEE Transactions on NanoBioscience10.1109/TNB.2023.328440623:1(81-90)Online publication date: Jan-2024
https://doi.org/10.1109/TNB.2023.3284406
Goshkoder DPolyanskii NVorobyev I(2024)Codes Correcting Long Duplication ErrorsIEEE Transactions on Molecular, Biological, and Multi-Scale Communications10.1109/TMBMC.2024.340375510:2(272-288)Online publication date: Jun-2024
https://doi.org/10.1109/TMBMC.2024.3403755
Nassirpour SShomorony IVahid A(2024)DNA Merge-Sort: A Family of Nested Varshamov-Tenengolts Reassembly Codes for Out-of-Order MediaIEEE Transactions on Communications10.1109/TCOMM.2023.333540972:3(1303-1317)Online publication date: Mar-2024
https://doi.org/10.1109/TCOMM.2023.3335409
Xiang LLiu QChen SYan KWu WYang K(2024)A Tutorial on Coding Methods for DNA-Based Molecular Communications and StorageIEEE Internet of Things Journal10.1109/JIOT.2023.333290311:7(11825-11847)Online publication date: 1-Apr-2024
https://doi.org/10.1109/JIOT.2023.3332903
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