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Improved read/write cost tradeoff in DNA-based data storage using LDPC codes [article]

Shubham Chandak, Kedar Tatwawadi, Billy Lau, Jay Mardia, Matthew Kubit, Joachim Neu, Peter Griffin, Mary Wootters, Tsachy Weissman, Hanlee Ji
2019 bioRxiv   pre-print
Recent advances in DNA sequencing and synthesis pipelines have made DNA-based storage a promising candidate for the storage technology of the future.Recently, there have been multiple efforts in this direction  ...  In this context, DNA-based storage systems can offer significantly higher storage densities (petabytes/gram) and durability (thousands of years) than current technologies.  ...  Funding We acknowledge funding from NSF/SRC (award number 1807371) under the SemiSynBio program and from Beck-  ... 
doi:10.1101/770032 fatcat:teq7iaduibdadptdbwqqnvdr2m

Modelling, characterization of data-dependent and process-dependent errors in DNA data storage [article]

Wang Yixin, MD Noor Rahim, Erry Gunawan, Yong Liang Guan, Chueh Loo Poh
2021 bioRxiv   pre-print
The results presented here introduce a more comprehensive channel model and offer a new angle towards the data recovery issue in DNA data storage by further elucidating the error characteristics of the  ...  Furthermore, we extensively explored several data-dependent unevenness observed in the base error patterns and studied a few potential factors and their impacts on the data imperfection at the decoder  ...  We thank Ng Yi Mei for assisting on the initial analysis. Funding  ... 
doi:10.1101/2021.07.17.452779 fatcat:26onxygjznbrxk7ltejs4bsnam

Optimized Code Design for Constrained DNA Data Storage with Asymmetric Errors

Li Deng, Yixin Wang, Md. Noor-A-Rahim, Yong Liang Guan, Zhiping Shi, Erry Gunawan, Chueh Loo Poh
2019 IEEE Access  
Limited by the current biochemical techniques, data might be corrupted during the processes of DNA data storage.  ...  Based on the analyses of the different asymmetric DNA sequencer channel models, a series of the protograph LDPC codes are optimized using a modified extrinsic information transfer algorithm (EXIT).  ...  ). 1 Second, we further optimize the protograph LDPC codes in this hybrid coding system based on the capacity analysis of the asymmetric DNA data storage channel.  ... 
doi:10.1109/access.2019.2924827 fatcat:gk7o4nkyprg4bhjeaaychsadfi

The Essential Component in DNA-Based Information Storage System: Robust Error-Tolerating Module

Aldrin Kay-Yuen Yim, Allen Chi-Shing Yu, Jing-Woei Li, Ada In-Chun Wong, Jacky F. C. Loo, King Ming Chan, S. K. Kong, Kevin Y. Yip, Ting-Fung Chan
2014 Frontiers in Bioengineering and Biotechnology  
The size of digital data is ever increasing and is expected to grow to 40,000 EB by 2020, yet the estimated global information storage capacity in 2011 is <300 EB, indicating that most of the data are  ...  Here, we suggested improvements on error handling methodology that could enable the integration of DNAbased computational process, e.g., algorithms based on self-assembly of DNA.  ...  LIMITATIONS ON CURRENTLY PROPOSED STORAGE SYSTEMS There are limitations on the existing DNA-based information storage system.  ... 
doi:10.3389/fbioe.2014.00049 pmid:25414846 pmcid:PMC4222239 fatcat:7imskryrznf2xgj7yfdvlqcf4q

Natural Data Storage: A Review on sending Information from now to then via Nature [article]

Dixita Limbachiya, Manish K. Gupta
2015 arXiv   pre-print
This article discuss DNA based information storage system in detail along with an overview about bacterial and protein data storage systems.  ...  As an alternative, researcher used natural medium of storage like DNA, bacteria and protein as information storage systems.  ...  Capacity of DNA under the substitution [Balado 2010 ], insertion and deletion error [Balado 2013 ] was proposed by F. Balado.  ... 
arXiv:1505.04890v1 fatcat:5bjrsgye5na5zpe67bvhp65hji

Concatenated Code Design for Constrained DNA Data Storage with Asymmetric Errors [article]

Yixin Wang, Li Deng, Md. Noor-A-Rahim, Erry Gunawan, Yong L. Guan, Zhi P. Shi, Chueh L. Poh
2021 arXiv   pre-print
asymmetric nucleotide level (i.e., A/T/C/G) substitution errors that may occur in the process of DNA sequencing.  ...  DNA Data storage has recently attracted much attention due to its durable preservation and extremely high information density (bits per gram) properties.  ...  on practical code design for DNA data storage.  ... 
arXiv:2112.09417v1 fatcat:mkocvq7dkfa45lugapzqyblbf4

RNA as a Nanoscale Data Transmission Medium: Error Analysis [article]

Andrew W. Eckford, Taro Furbayashi, Tadashi Nakano
2016 arXiv   pre-print
This paper presents an error analysis for RNA as a data transmission medium, analyzing how deletion errors increase in a collection of replicated DNA strands over time.  ...  RNA can be used as a high-density medium for data storage and transmission; however, an important RNA process -- replication -- is noisy.  ...  The extremely high density and stability of DNA/RNA-based data storage makes it a potential solution for data storage and data transmission applications [1] .  ... 
arXiv:1609.07329v1 fatcat:qpkv2ux3p5bzhcgrwzoovhgjsq

High capacity DNA data storage with variable-length Oligonucleotides using repeat accumulate code and hybrid mapping

Yixin Wang, Md Noor-A-Rahim, Jingyun Zhang, Erry Gunawan, Yong Liang Guan, Chueh Loo Poh
2019 Journal of Biological Engineering  
the practical implementation of DNA data storage with high capacity.  ...  The advancement reported would move us closer to achieving a practical high-capacity DNA data storage system.  ...  Availability of data and material The data that support the results of this study are available from the corresponding authors upon reasonable request.  ... 
doi:10.1186/s13036-019-0211-2 pmid:31832092 pmcid:PMC6868767 fatcat:7aplsrmczjamvcmh2m23d2nmoi

SPIDER-WEB enables stable, repairable, and encryptible algorithms under arbitrary local biochemical constraints in DNA-based storage [article]

Haoling Zhang, Zhaojun Lan, Wenwei Zhang, Xun Xu, Zhi Ping, Yiwei Zhang, Yue Shen
2022 arXiv   pre-print
Despite the biochemical progress in DNA synthesis and sequencing, novel coding algorithms need to be constructed under the specific constraints in DNA-based storage.  ...  To further consider recovery and security issues existing in the storage field, it also provides pluggable algorithmic patches based on the generated coding algorithms: path-based correcting and mapping  ...  The data is the sub-data (100nt/1%) of Figure 5 . • 0% Figure. 1 . 1 Figure. 1. Pipelines and operations in DNA-based storage.  ... 
arXiv:2204.02855v2 fatcat:buae2g7ojfacbi7uebwjcayeki

A modified watermark synchronisation code for robust embedding of data in DNA

David Haughton, Felix Balado
2013 2013 IEEE International Conference on Acoustics, Speech and Signal Processing  
INTRODUCTION Recent advances in technology have enabled the use of DNA in novel ways, such as highly parallel computing and data storage.  ...  The base substitution mutation model used here, called the Kimura model of molecular evolution [12] , reflects that DNA bases belong to one of two chemically distinct groups: purines, R = {A, G} or pyrimidines  ... 
doi:10.1109/icassp.2013.6637830 dblp:conf/icassp/HaughtonB13 fatcat:7iwrcxkbmjbf7gihnsqdsnsu5u

Efficient storage of high throughput DNA sequencing data using reference-based compression

M. Hsi-Yang Fritz, R. Leinonen, G. Cochrane, E. Birney
2011 Genome Research  
Data storage costs have become an appreciable proportion of total cost in the creation and analysis of DNA sequence data.  ...  Of particular concern is that the rate of increase in DNA sequencing is significantly outstripping the rate of increase in disk storage capacity.  ...  Charles Cook provided invaluable proofreading of the manuscript. The authors were funded by EMBL core funds. The SRA archive is supported by the Wellcome Trust.  ... 
doi:10.1101/gr.114819.110 pmid:21245279 pmcid:PMC3083090 fatcat:3wtom5xn2zdnzja6apbbppceby

DNA nanotechnology: new adventures for an old warhorse

Bijan Zakeri, Timothy K Lu
2015 Current Opinion in Chemical Biology  
Highlights 19 • Advances in DNA synthesis have provided new opportunities for DNA 20 nanotechnology. 21 • DNA has several key attributes that make it ideal for storing digital data. 22  ...  the local humidity around DNA and aiding in long-term stability. 202 Based on their error-correction and silica storage methods, the authors estimated 203 that digital data stored in DNA could be recovered  ...  and 178 then shipping the DNA around the world under standard conditions, the authors 179 demonstrated the versatility of DNA for not only information storage but also for 180 stability under everyday  ... 
doi:10.1016/j.cbpa.2015.05.020 pmid:26056949 pmcid:PMC4818966 fatcat:5na4ifwhdvgrrauexokt2tanbm

Information-Theoretic Foundations of DNA Data Storage

Ilan Shomorony, Reinhard Heckel
2022 Foundations and Trends in Communications and Information Theory  
need of data storage.  ...  While in living things, DNA molecules can consist of millions of nucleotides, due to technological constraints, in practice, data is stored on many short DNA molecules, which are preserved in a DNA pool  ...  Last but not least, the DNA molecules in a DNA-based storage system are subject to errors such as insertions, deletions, and substitutions of nucleotides at the time of synthesis, during the storage period  ... 
doi:10.1561/0100000117 fatcat:2sxmsdcd6ff7dgqwnp2p4nvsw4

Carbon-based archiving: current progress and future prospects of DNA-based data storage

Zhi Ping, Dongzhao Ma, Xiaoluo Huang, Shihong Chen, Longying Liu, Fei Guo, Sha Joe Zhu, Yue Shen
2019 GigaScience  
This review summarizes state-of-the-art methods, including digital-to-DNA coding schemes and the media types used in DNA-based data storage, and provides an overview of recent progress achieved in this  ...  Indeed, DNA-based data storage has recently emerged as a promising approach for long-term digital information storage.  ...  In addition, the scale of DNA synthesis also affects the information capacity of DNA-based data storage per unit mass.  ... 
doi:10.1093/gigascience/giz075 pmid:31220251 pmcid:PMC6586197 fatcat:bn3bfpgaqneqzpge2iot6hmohe

DNA Storage: A Promising Large Scale Archival Storage? [article]

Yixun Wei, Bingzhe Li, David H.C. Du
2022 arXiv   pre-print
However, according to our investigation, DNA storage tube capacity based on the current synthesizing and sequencing technologies is only at hundreds of Gigabytes due to the limitation of multiple bio and  ...  Several studies have verified the feasibility of using DNA for archival storage with a small amount of data.  ...  However, the achievable storage capacity of using DNA for archive based on current biotechnologies remains unknown. In DNA storage, Data is in the form of powder for a longer duration.  ... 
arXiv:2204.01870v2 fatcat:4yuvc35oajcofaddtificrjwn4
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