Promiscuous molecules for smarter file operations in DNA-based data storage

AbstractDNA holds significant promise as a data storage medium due to its density, longevity, and resource and energy conservation. These advantages arise from the inherent biomolecular structure of DNA which differentiates it from conventional storage media. The unique molecular architecture of DNA storage also prompts important discussions on how data should be organized, accessed, and manipulated and what practical functionalities may be possible. Here we leverage thermodynamic tuning of biomolecular interactions to implement useful data access and organizational features. Specific sets of environmental conditions including distinct DNA concentrations and temperatures were screened for their ability to switchably access either all DNA strands encoding full image files from a GB-sized background database or subsets of those strands encoding low resolution, File Preview, versions. We demonstrate File Preview with four JPEG images and provide an argument for the substantial and practical economic benefit of this generalizable strategy to organize data.

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A Quaternary Code Correcting a Burst of at Most Two Deletion or Insertion Errors in DNA Storage

Entropy ◽

10.3390/e23121592 ◽

2021 ◽

Vol 23 (12) ◽

pp. 1592

Author(s):

Thi-Huong Khuat ◽

Sunghwan Kim

Keyword(s):

Error Correction ◽

Data Storage ◽

Upper Bounds ◽

Code Design ◽

Lower And Upper Bounds ◽

Decoding Algorithms ◽

Quaternary Code ◽

Quaternary Codes ◽

Dna Storage ◽

Dna Strands

Due to the properties of DNA data storage, the errors that occur in DNA strands make error correction an important and challenging task. In this paper, a new code design of quaternary code suitable for DNA storage is proposed to correct at most two consecutive deletion or insertion errors. The decoding algorithms of the proposed codes are also presented when one and two deletion or insertion errors occur, and it is proved that the proposed code can correct at most two consecutive errors. Moreover, the lower and upper bounds on the cardinality of the proposed quaternary codes are also evaluated, then the redundancy of the proposed code is provided as roughly 2log48n.

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On Models and Capacity Bounds for DNA-based Storage Channels

10.36227/techrxiv.16633561.v1 ◽

2021 ◽

Author(s):

Zihui Yan ◽

Cong Liang

Keyword(s):

Data Storage ◽

Storage System ◽

Synchronization Error ◽

Dna Molecules ◽

Capacity Limits ◽

Dna Storage ◽

Capacity Bounds ◽

Dna Strands ◽

Term Data

In recent years, DNA-based systems have become a promising medium for long-term data storage. There are two layers of errors in DNA-based storage systems. The first is the dropouts of the DNA strands, which has been characterized in the shuffling-sampling channel. The second is insertions, deletions, and substitutions of nucleotides in individual DNA molecules. In this paper, we describe a DNA noisy synchronization error channel to characterize the errors in individual DNA molecules. We derive non-trivial lower and upper capacity bounds of the DNA noisy synchronization error channel based on information theory. By cascading these two channels, we provide theoretical capacity limits of the DNA storage system. These results reaffirm that DNA is a reliable storage medium with high storage density potential.

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Implementasi Network Attached Storage (NAS) Menggunakan Freenas Pada STMIK Lombok

Jurnal Manajemen Informatika dan Sistem Informasi ◽

10.36595/misi.v1i1.11 ◽

2018 ◽

Vol 1 (1) ◽

pp. 6

Author(s):

Lalu Supriadi Kalaena ◽

Wire Bagye

Keyword(s):

Data Storage ◽

Network Architecture ◽

Local Area Network ◽

Data Access ◽

Local Network ◽

Storage Device ◽

Area Network ◽

Process Data ◽

Storage Media ◽

Network Attached Storage

STMIK Lombok is an institution engaged in education that process data, about students, student practical data, lecturer data, and correspondence. Media file storage applied STMIK Lombok still on a separate computer, both academic data and practical data, so to access the file must be done on the computer where the storage. Based on the capability of Network Attached Storage in local network, by looking at the need of data storage media on the network at STMIK Lombok and the observation result then designed a network architecture by utilizing Network Attached Storage device with focus on fast storage and data transfer process. Stages of research include Data collection, design, and methods of testing To be able to help solve the problem of separate data access then implemented Network Attached Storage (NAS) which is a network to perform distribution of storage assets owned by the server of a network system that has the advantage of faster access to data stored through Local Area Network, minimal cost and cheap and easy maintenance, from setup to configuration, and available Open Source Software. After doing the testing phase it can be concluded that FreeNas as an operating system used for the processing of network storage media is very capable of handling the task well and the facilities that exist in it is very supportive in storage and accessing files. FreeNas web is very helpful and allows users to configure it other than it can be used without having to spend a large cost, and with the facilities in the FreeNas.

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Driving the scalability of DNA-based information storage systems

10.1101/591594 ◽

2019 ◽

Author(s):

Kyle J. Tomek ◽

Kevin Volkel ◽

Alexander Simpson ◽

Austin G. Hass ◽

Elaine W. Indermaur ◽

...

Keyword(s):

Data Storage ◽

Storage Systems ◽

Information Storage ◽

Maximum Capacity ◽

Theoretical Maximum ◽

New Approaches ◽

File Access ◽

Storage Media ◽

Dna Storage ◽

Address System

ABSTRACTThe extreme density of DNA presents a compelling advantage over current storage media; however, in order to reach practical capacities, new approaches for organizing and accessing information are needed. Here we use chemical handles to selectively extract unique files from a complex database of DNA mimicking 5 TB of data and design and implement a nested file address system that increases the theoretical maximum capacity of DNA storage systems by five orders of magnitude. These advancements enable the development and future scaling of DNA-based data storage systems with reasonable modern capacities and file access capabilities.

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On Models and Capacity Bounds for DNA-based Storage Channels

10.36227/techrxiv.16633561 ◽

2021 ◽

Author(s):

Zihui Yan ◽

Cong Liang

Keyword(s):

Data Storage ◽

Storage System ◽

Synchronization Error ◽

Dna Molecules ◽

Capacity Limits ◽

Dna Storage ◽

Capacity Bounds ◽

Dna Strands ◽

Term Data

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Combinatorial constraint coding based on the EORS algorithm in DNA storage

PLoS ONE ◽

10.1371/journal.pone.0255376 ◽

2021 ◽

Vol 16 (7) ◽

pp. e0255376

Author(s):

Li Xiaoru ◽

Guo Ling

Keyword(s):

Data Storage ◽

Hamming Distance ◽

Random Search ◽

Gc Content ◽

Information Storage ◽

Storage Media ◽

Specific Hybridization ◽

Dna Storage ◽

Electronic Storage ◽

Increasing Demand

The development of information technology has produced massive amounts of data, which has brought severe challenges to information storage. Traditional electronic storage media cannot keep up with the ever-increasing demand for data storage, but in its place DNA has emerged as a feasible storage medium with high density, large storage capacity and strong durability. In DNA data storage, many different approaches can be used to encode data into codewords. DNA coding is a key step in DNA storage and can directly affect storage performance and data integrity. However, since errors are prone to occur in DNA synthesis and sequencing, and non-specific hybridization is prone to occur in the solution, how to effectively encode DNA has become an urgent problem to be solved. In this article, we propose a DNA storage coding method based on the equilibrium optimization random search (EORS) algorithm, which meets the Hamming distance, GC content and no-runlength constraints and can reduce the error rate in storage. Simulation experiments have shown that the size of the DNA storage code set constructed by the EORS algorithm that meets the combination constraints has increased by an average of 11% compared with previous work. The increase in the code set means that shorter DNA chains can be used to store more data.

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NOREC4DNA: using near-optimal rateless erasure codes for DNA storage

BMC Bioinformatics ◽

10.1186/s12859-021-04318-x ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Peter Michael Schwarz ◽

Bernd Freisleben

Keyword(s):

Data Storage ◽

Dna Sequences ◽

Storage Systems ◽

High Capacity ◽

Digital Data ◽

Erasure Codes ◽

Software Framework ◽

Digital Information ◽

Dna Storage ◽

Dna Strands

Abstract Background DNA is a promising storage medium for high-density long-term digital data storage. Since DNA synthesis and sequencing are still relatively expensive tasks, the coding methods used to store digital data in DNA should correct errors and avoid unstable or error-prone DNA sequences. Near-optimal rateless erasure codes, also called fountain codes, are particularly interesting codes to realize high-capacity and low-error DNA storage systems, as shown by Erlich and Zielinski in their approach based on the Luby transform (LT) code. Since LT is the most basic fountain code, there is a large untapped potential for improvement in using near-optimal erasure codes for DNA storage. Results We present NOREC4DNA, a software framework to use, test, compare, and improve near-optimal rateless erasure codes (NORECs) for DNA storage systems. These codes can effectively be used to store digital information in DNA and cope with the restrictions of the DNA medium. Additionally, they can adapt to possible variable lengths of DNA strands and have nearly zero overhead. We describe the design and implementation of NOREC4DNA. Furthermore, we present experimental results demonstrating that NOREC4DNA can flexibly be used to evaluate the use of NORECs in DNA storage systems. In particular, we show that NORECs that apparently have not yet been used for DNA storage, such as Raptor and Online codes, can achieve significant improvements over LT codes that were used in previous work. NOREC4DNA is available on https://github.com/umr-ds/NOREC4DNA. Conclusion NOREC4DNA is a flexible and extensible software framework for using, evaluating, and comparing NORECs for DNA storage systems.

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