scholarly journals Addition of Degenerate Bases to DNA-based Data Storage for Increased Information Capacity

2018 ◽  
Author(s):  
Yeongjae Choi ◽  
Taehoon Ryu ◽  
Amos C. Lee ◽  
Hansol Choi ◽  
Hansaem Lee ◽  
...  

Introductory paragraphDNA-based data storage has emerged as a promising method to satisfy the exponentially increasing demand for information storage. However, practical implementation of DNA-based data storage remains a challenge because of the high cost of DNA per unit data. Here, we propose the use of eleven degenerate bases as encoding characters in addition to A, C, G, and T, which increases the information capacity (the amount of data that can be stored per length of DNA sequence designed) and reduce the cost of DNA per unit data. Using the proposed method, we experimentally achieved an information capacity of 3.37 bits/character, which is more than twice when compared to the highest information capacity previously achieved. Finally, the platform was projected to reduce the cost of DNA-based data storage by 50%.

Author(s):  
Vladimir Meikshan ◽  
◽  
Natalia Teslya ◽  

Benefits of using cloud technology are obvious, their application is expanding, as a result, it determines the steady growth of demand. Cloud computing has acquired particular relevance for large companies connected with Internet services, retailing, logistics that generate large volume of business and other information. The use of cloud technologies allows organizing the joint consumption of resources, solving the problems of storing and transferring significant amounts of data. Russian consumer cooperation refers to large territory distributed organizations actively forming their own digital ecosystem. The issue of data storing and processing for consumer coo-peration organizations is very relevant. At the same time, the prices of cloud service providers are significantly different and require solving the problem of minimizing the cost of storing and transferring significant amounts of data. The application of the linear programming method is considered to select the optimal data storage scheme for several cloud service providers having different technical and economic parameters of the package (maximum amount of storage, cost of allocated resources). Mathematical model includes the equation of costs for data storing and transferring and restrictions on the amount of storage, the amount of data and its safety. Software tool that allows to perform numerical calculations is selected Microsoft Excel in combination with the "search for solutions" add-on. In accordance with the mathematical model, the conditions for minimizing the amount of cloud storage costs and the necessary restrictions are established. Initial data are set for three data forming centers, storages of certain size for five cloud service providers and nominal price for information storage and transmission. Calculations of expenses are performed in several variants: without optimization, with the solution of the optimization problem, with price increase by cloud service providers. Results of the calculations confirm the necessity to solve the problem of minimizing the cost of cloud services for corporate clients. The presented model can be expanded for any cost conditions as well as for different areas of cloud applications.


Author(s):  
Stanislav Kruglik ◽  
Gregory Kucherov ◽  
Kamilla Nazirkhanova ◽  
Mikhail Filitov

Introduction: Currently, we witness an explosive growth in the amount of information produced by humanity. This raises new fundamental problems of its efficient storage and processing. Commonly used magnetic, optical, and semiconductor information storage devices have several drawbacks related to small information density and limited durability. One of the promising novel approaches to solving these problems is DNA-based data storage. Purpose: An overview of modern DNA-based storage systems and related information-theoretic problems. Results: The current state of the art of DNA-based storage systems is reviewed. Types of errors occurring in them as well as corresponding error-correcting codes are analized. The disadvantages of these codes are shown, and possible pathways for improvement are mentioned. Proposed information-theoretic models of DNA-based storage systems are analyzed, and their limitation highlighted. In conclusion, main obstacles to practical implementation of DNA-based storage systems are formulated, which can be potentially overcome using information-theoretic methods considered in this overview.


2019 ◽  
Vol 13 (1) ◽  
Author(s):  
Yixin Wang ◽  
Md Noor-A-Rahim ◽  
Jingyun Zhang ◽  
Erry Gunawan ◽  
Yong Liang Guan ◽  
...  

Abstract Background With the inherent high density and durable preservation, DNA has been recently recognized as a distinguished medium to store enormous data over millennia. To overcome the limitations existing in a recently reported high-capacity DNA data storage while achieving a competitive information capacity, we are inspired to explore a new coding system that facilitates the practical implementation of DNA data storage with high capacity. Result In this work, we devised and implemented a DNA data storage scheme with variable-length oligonucleotides (oligos), where a hybrid DNA mapping scheme that converts digital data to DNA records is introduced. The encoded DNA oligos stores 1.98 bits per nucleotide (bits/nt) on average (approaching the upper bound of 2 bits/nt), while conforming to the biochemical constraints. Beyond that, an oligo-level repeat-accumulate coding scheme is employed for addressing data loss and corruption in the biochemical processes. With a wet-lab experiment, an error-free retrieval of 379.1 KB data with a minimum coverage of 10x is achieved, validating the error resilience of the proposed coding scheme. Along with that, the theoretical analysis shows that the proposed scheme exhibits a net information density (user bits per nucleotide) of 1.67 bits/nt while achieving 91% of the information capacity. Conclusion To advance towards practical implementations of DNA storage, we proposed and tested a DNA data storage system enabling high potential mapping (bits to nucleotide conversion) scheme and low redundancy but highly efficient error correction code design. The advancement reported would move us closer to achieving a practical high-capacity DNA data storage system.


PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0255376
Author(s):  
Li Xiaoru ◽  
Guo Ling

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.


2021 ◽  
Vol 21 ◽  
pp. 378-382
Author(s):  
Dominika Kornaś

This article presents a comparison of data storage methods available in the Android SDK. Analyzes the following information storage methods: SQLite, Room, Content Providers, SharedPreferences and DataStore. It examines the relationship between the complexity of the data structure and the cost and efficiency of data storage with the use of given methods. Presents the results of the performance test and conclusions drawn from their analysis.


Author(s):  
V. A. Minaev ◽  
A. V. Mazin ◽  
K. B. Zdiruk ◽  
L. S. Kulikov

The article presents the scientific and methodological issues of formation of digital twins collections based on the use of the multi-aspect recursive decomposition algorithm of the subject area. The general approaches to the solution of topical issues of the modern stage of artificial intelligence are considered. The terminology is concretized in the interrelated areas of knowledge – information – data and its relation with the term of «digital twins» as information containers of knowledge is discussed. The structure, power estimation and metrizability of the information space presented as a recursively defined ordered set of elements – a collection of digital twins (DT-collections) are considered. It is shown that the practical implementation of this approach and its application as part of automated control systems involves maintaining the life cycle of the creation and operation of digital twins in the Integrated information storage, implementing a two-circuit scheme (model) of management. A new cognitive approach to assess the completeness of the knowledge measure in the information space is proposed. The model of the integrated information storage realizing accumulation of knowledge in data banks of primary and secondary information is considered. As an example, a recursive decomposition of a subset of engineering systems of an educational institution is performed.


2019 ◽  
Vol 15 (01) ◽  
pp. 1-8
Author(s):  
Ashish C Patel ◽  
C G Joshi

Current data storage technologies cannot keep pace longer with exponentially growing amounts of data through the extensive use of social networking photos and media, etc. The "digital world” with 4.4 zettabytes in 2013 has predicted it to reach 44 zettabytes by 2020. From the past 30 years, scientists and researchers have been trying to develop a robust way of storing data on a medium which is dense and ever-lasting and found DNA as the most promising storage medium. Unlike existing storage devices, DNA requires no maintenance, except the need to store at a cool and dark place. DNA has a small size with high density; just 1 gram of dry DNA can store about 455 exabytes of data. DNA stores the informations using four bases, viz., A, T, G, and C, while CDs, hard disks and other devices stores the information using 0’s and 1’s on the spiral tracks. In the DNA based storage, after binarization of digital file into the binary codes, encoding and decoding are important steps in DNA based storage system. Once the digital file is encoded, the next step is to synthesize arbitrary single-strand DNA sequences and that can be stored in the deep freeze until use.When there is a need for information to be recovered, it can be done using DNA sequencing. New generation sequencing (NGS) capable of producing sequences with very high throughput at a much lower cost about less than 0.1 USD for one MB of data than the first sequencing technologies. Post-sequencing processing includes alignment of all reads using multiple sequence alignment (MSA) algorithms to obtain different consensus sequences. The consensus sequence is decoded as the reversal of the encoding process. Most prior DNA data storage efforts sequenced and decoded the entire amount of stored digital information with no random access, but nowadays it has become possible to extract selective files (e.g., retrieving only required image from a collection) from a DNA pool using PCR-based random access. Various scientists successfully stored up to 110 zettabytes data in one gram of DNA. In the future, with an efficient encoding, error corrections, cheaper DNA synthesis,and sequencing, DNA based storage will become a practical solution for storage of exponentially growing digital data.


Author(s):  
Hong Guo

Many new media technologies have emerged in modern society. The application of new media technologies has impacted traditional TV news media, which not only faces great challenges, but also brings some lessons for the development of TV news media. New media technology relies on powerful information processing technology and data storage technology to develop and grow continuously. Compared with traditional news, new media technology has more powerful information storage capacity and dissemination capacity. Firstly, this paper briefly introduces the concept of new media technology, summarizes the typical characteristics of new media technology, and analyzes the existing problems in the application of new media technology in the news communication industry based on the necessity of applying new media technology. Finally, some Suggestions are put forward based on this, hoping to provide some reference for the development of news communication industry.


2003 ◽  
Vol 788 ◽  
Author(s):  
Andrei A. Eliseev ◽  
Kirill S. Napolskii ◽  
Dmitry F. Gorozhankin ◽  
Alexei V. Lukashin ◽  
Yuri D. Tretyakov ◽  
...  

ABSTRACTHere we report the synthesis and investigation of iron and iron oxide nanowire arrays using mesoporous silica as a host material. In the present work a novel variant of synthesis of ordered magnetic nanowires in the mesoporous silica matrix was suggested. The method is based on the incorporation of a hydrophobic metal compound into the hydrophobic part of silica-surfactant composite. The amount of iron intercalated into the mesoporous matrix was measured by chemical analysis. In all samples it corresponds well to with the molar ratio SiO2: Fe = 9:1. To provide crystallinity of nanowires additional thermal treatment was performed. Thus prepared nanocomposites were characterized by TEM, ED, SAXS, SANS, BET and magnetic measurements. The anisotropy parameters of nanowires were determined using two non-correlated methods: temperature dependence of magnetic susceptibility and small angle polarized neutron scattering. It was found that the particle length increases with the increasing of the decomposition temperature of the metal complex. Obviously it deals with crystallization and growth of metal particles inside the pores at a constant diameter of a single particle. For iron containing sample annealed at 375 °C (form factor of nanowire is about 40), the coercive force at room temperature was found to be 145 Oe at saturation magnetization of 1.2 emu/g, which is not far from modern information storage. It was shown that particles shape and size are in good agreement with that of the pores. Particles are uniform and well ordered in the silica matrix. Thus, the suggested method leads to one-dimensional anisotropic nanostructures which could find an application as high-density data storage magnetic media.


2014 ◽  
Vol 513-517 ◽  
pp. 2107-2110 ◽  
Author(s):  
Zhi Jian Diao ◽  
Song Guo

Cloud computing is a novel network-based computing model, in which the cloud infrastructure is constructed in bottom level and provided as the support environment for the applications in upper cloud level. The combination of clouding computing and GIS can improve the performance of GIS, and it can also provide a new prospect of GIS information storage, processing and utilization. By integrating cloud computing and GIS, this paper presented a cloud computing based GIS model based on two features of cloud computing: data storage and transparent custom service. The model contains two layers: service layer and application layer. With this two-layer model, GIS can provide stable and efficient services to end users by optimized network resource allocation of underlying data and services in cloud computing.


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