181 results on '"Digital Data Storage"'
Search Results
2. Uncertainties in synthetic DNA-based data storage
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Biao Ma, Chao Zhao, Chengtao Xu, and Hong Liu
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0303 health sciences ,AcademicSubjects/SCI00010 ,business.industry ,Information Storage and Retrieval ,DNA ,02 engineering and technology ,Data loss ,Biology ,021001 nanoscience & nanotechnology ,Replication (computing) ,Field (computer science) ,03 medical and health sciences ,Digital Data Storage ,Data redundancy ,Data integrity ,Computer data storage ,Genes, Synthetic ,Genetics ,Biochemical engineering ,Survey and Summary ,0210 nano-technology ,business ,Error detection and correction ,030304 developmental biology - Abstract
Deoxyribonucleic acid (DNA) has evolved to be a naturally selected, robust biomacromolecule for gene information storage, and biological evolution and various diseases can find their origin in uncertainties in DNA-related processes (e.g. replication and expression). Recently, synthetic DNA has emerged as a compelling molecular media for digital data storage, and it is superior to the conventional electronic memory devices in theoretical retention time, power consumption, storage density, and so forth. However, uncertainties in the in vitro DNA synthesis and sequencing, along with its conjugation chemistry and preservation conditions can lead to severe errors and data loss, which limit its practical application. To maintain data integrity, complicated error correction algorithms and substantial data redundancy are usually required, which can significantly limit the efficiency and scale-up of the technology. Herein, we summarize the general procedures of the state-of-the-art DNA-based digital data storage methods (e.g. write, read, and preservation), highlighting the uncertainties involved in each step as well as potential approaches to correct them. We also discuss challenges yet to overcome and research trends in the promising field of DNA-based data storage.
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- 2021
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3. DNA; Digital Data Storage Device
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Kavia V
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Digital Data Storage ,chemistry.chemical_compound ,chemistry ,Computer science ,business.industry ,Word error rate ,business ,Computer hardware ,DNA - Published
- 2021
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4. An Overview of<scp>DNA</scp>‐Based Digital Data Storage
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John H. Reif, Shalin Shah, and Xin Song
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Digital Data Storage ,chemistry.chemical_compound ,chemistry ,Computer science ,business.industry ,business ,DNA ,Computer hardware - Published
- 2021
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5. Quantifying molecular bias in DNA data storage
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Christopher N. Takahashi, Kendall Stewart, Karin Strauss, Yuan-Jyue Chen, Bill Peck, Georg Seelig, Luis Ceze, Lee Organick, Siena Dumas Ang, and Patrick Weiss
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0301 basic medicine ,Process (engineering) ,Computer science ,Sequence analysis ,Science ,DNA digital data storage ,Digital data ,Information Storage and Retrieval ,General Physics and Astronomy ,Computational biology ,02 engineering and technology ,Oligonucleotide synthesis ,computer.software_genre ,Article ,General Biochemistry, Genetics and Molecular Biology ,law.invention ,chemistry.chemical_compound ,03 medical and health sciences ,Bias ,law ,Redundancy (engineering) ,A-DNA ,DNA sequencing ,lcsh:Science ,Polymerase chain reaction ,Synthetic biology ,Multidisciplinary ,Oligonucleotide ,Provisioning ,Statistical model ,Sequence Analysis, DNA ,General Chemistry ,Models, Theoretical ,021001 nanoscience & nanotechnology ,Digital Data Storage ,030104 developmental biology ,chemistry ,lcsh:Q ,Data mining ,0210 nano-technology ,computer ,DNA ,DNA computing and cryptography - Abstract
DNA has recently emerged as an attractive medium for archival data storage. Recent work has demonstrated proof-of-principle prototype systems; however, very uneven (biased) sequencing coverage has been reported, which indicates inefficiencies in the storage process. Deviations from the average coverage in the sequence copy distribution can either cause wasteful provisioning in sequencing or excessive number of missing sequences. Here, we use millions of unique sequences from a DNA-based digital data archival system to study the oligonucleotide copy unevenness problem and show that the two paramount sources of bias are the synthesis and amplification (PCR) processes. Based on these findings, we develop a statistical model for each molecular process as well as the overall process. We further use our model to explore the trade-offs between synthesis bias, storage physical density, logical redundancy, and sequencing redundancy, providing insights for engineering efficient, robust DNA data storage systems., DNA is an attractive digital data storing medium due to high information density and longevity. Here the authors use millions of sequences to investigate inherent biases in DNA synthesis and PCR amplification.
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- 2020
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6. Dealing With Technological Trajectories: Where We Have Come From and Where We Are Going
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Katina Michael, Samuel Fosso-Wamba, Eusebio Scornavacca, Roba Abbas, and George Roussos
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Digital Data Storage ,Civilization ,Computer science ,business.industry ,Technological change ,Human life ,media_common.quotation_subject ,Key (cryptography) ,Clothing ,business ,Data science ,media_common ,Simple (philosophy) - Abstract
Technological progress is widely recognized as having considerable impact on human societies, which have become more and more dependent on human-made tools that entail intricate scientific processes, considered technology [item 1) in the Related Works]. The adoption of such tools is borne out of the necessity of survival at first [item 2) in the Related Works], and subsequently as a means to improve access to food, shelter, and clothing; arguably things that we cannot live without. Nevertheless, the urgency of understanding the role of technology in human life has never been as vital as today. Indeed, one could say that technological progress is the key ingredient driving human civilization: the invention of ever more complex tools traces the history of human civilization and its development. Each generation of technology lays the foundation for the next, the invention of simple machines, such as the wheel, for example, enabled the invention of the wheelbarrow, which enabled in turn building larger structures. In parallel, the wheel enabled the construction of gears to transmit power from crankshaft to driveshaft and also the rotation of magnetic tapes permitting the capture of binary data leading to the spinning hard disk drives and their superior digital data storage capacity.
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- 2020
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7. Forward Error Correction for DNA Data Storage.
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Blawat, Meinolf, Gaedke, Klaus, Huetter, Ingo, Chen, Xiao-Ming, Turczyk, Brian, Inverso, Samuel, Pruitt, Benjamin, and Church, George
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FORWARD error correction ,INFORMATION storage & retrieval systems ,ERROR analysis in mathematics ,ROBUST control ,DNA synthesis - Abstract
We are reporting on a strong capacity boost in storing digital data in synthetic DNA. In principle, synthetic DNA is an ideal media to archive digital data for very long times because the achievable data density and longevity outperforms today’s digital data storage media by far. On the other hand, neither the synthesis, nor the amplification and the sequencing of DNA strands can be performed error-free today and in the foreseeable future. In order to make synthetic DNA available as digital data storage media, forward-error-correction schemes have to be applied. In order to realize DNA data storage, we have developed an efficient and robust forward-error-correcting scheme adapted to the DNA channel. We based the design of the needed DNA channel model on data from a proof-of-concept conducted 2012 by a team from the Harvard Medical School*. Our forward error correction scheme is able to cope with all error types of today DNA synthesis, amplification and sequencing processes, e.g. insertion, deletion, and swap errors. In a successful experiment, we were able to store and retrieve error-free 22MByte of digital data in synthetic DNA recently. The found residual error probability is already in the same order as it is in hard disk drives and can be easily improved. This proves the feasibility to use synthetic DNA as a long-term digital data storage media. In an already planned next development step we will increase the amount of stored data into the GByte range. The presented forward error correction scheme is already designed for such and even much higher volumes of data.*) Church, G. M.; Gao, Y.; Kosuri, S. (2012). “Next-Generation Digital Information Storage in DNA”. Science 337 (6102): 1628 [ABSTRACT FROM AUTHOR]
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- 2016
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8. Survey on Asymmetric Cryptography Algorithms
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Tian Zhou, Zhaochun Sun, and Yifan Shen
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business.industry ,Computer science ,Key distribution ,Data_CODINGANDINFORMATIONTHEORY ,Encryption ,Public-key cryptography ,Digital Data Storage ,Digital signature ,Cryptosystem ,Hardware_ARITHMETICANDLOGICSTRUCTURES ,Elliptic curve cryptography ,business ,Algorithm ,ElGamal encryption - Abstract
Recent years have seen the importance of ensuring the safety and confidentiality of communication and digital data storage. Thus, secure cryptosystems are needed to guarantee security issues. Among them are asymmetric cryptography algorithms, which have been widely applied for carrying out key distribution and digital signature. This paper focuses on the current mainstream types of asymmetric cryptography, including the Rivest-Shamir-Adleman (RSA) algorithm, the Elgamal algorithm, and the Elliptic curve cryptography (ECC) algorithm, and discuss their characteristics, advantages as well as prospects, respectively.
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- 2021
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9. Data Anonymization Using Pseudonym System to Preserve Data Privacy
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Shukor Abd Razak, Nur Hafizah Mohd Nazari, and Arafat Al-Dhaqm
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Information privacy ,Authentication ,Spoofing attack ,General Computer Science ,Data anonymization ,Computer science ,business.industry ,General Engineering ,pseudonym ,palm vein ,Cloud computing ,unlinkability ,Computer security ,computer.software_genre ,Unique identifier ,Digital Data Storage ,Data access ,anonimous ,General Materials Science ,lcsh:Electrical engineering. Electronics. Nuclear engineering ,business ,computer ,lcsh:TK1-9971 ,data preserving - Abstract
Data collection and storage in a large size is done on a routine basis in any company or organization. To this end, wireless network infrastructure and cloud computing are two widely-used tools. With the use of such services, less time is needed to attain the required output, and also managing the jobs will be simpler for users. General services employ a unique identifier for the aim of storing data in a digital database. However, it may be associated with some limitations and challenges. There is a link between the unique identifier and the data holder, e.g., name, address, Identity card number, etc. Attackers can manipulate a unique identifier for stealing the whole data. To get the data needed, attackers may even eavesdrop or guess. It results in lack of data privacy protection. As a result, it is necessary to take into consideration the data privacy issues in any data digital data storage. With the use of current services, there is a high possibility of exposure and leak of data/information to an unauthorized party during their transfer process. In addition, attacks may take place against services; for instance spoofing attacks, forgery attacks, etc. in the course of information transaction. To address such risks, this paper suggests the use of a biometric authentication method by means of a palm vein during the authentication process. Furthermore, a pseudonym creation technique is adopted to make the database record anonymous, which can make sure the data is properly protected. This way, any unauthorized party cannot gain access to data/information. The proposed system can resolve the information leaked, the user true identity is never revealed to others.
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- 2020
10. DNA assembly for nanopore data storage readout
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Randolph Lopez, Miklos Z. Racz, Karin Strauss, Sergey Yekhanin, Yuan-Jyue Chen, Georg Seelig, Luis Ceze, Siena Dumas Ang, and Konstantin Makarychev
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0301 basic medicine ,Computer science ,DNA digital data storage ,Science ,General Physics and Astronomy ,Information Storage and Retrieval ,Nanotechnology ,02 engineering and technology ,General Biochemistry, Genetics and Molecular Biology ,Article ,03 medical and health sciences ,chemistry.chemical_compound ,Nanopores ,Databases, Genetic ,Sequencing ,DNA nanotechnology ,lcsh:Science ,Throughput (business) ,Multidisciplinary ,Nanoscale materials ,business.industry ,General Chemistry ,DNA ,Sequence Analysis, DNA ,Amplicon ,021001 nanoscience & nanotechnology ,Nanopore ,Digital Data Storage ,030104 developmental biology ,ComputingMethodologies_PATTERNRECOGNITION ,chemistry ,Computer data storage ,lcsh:Q ,Nanopore sequencing ,0210 nano-technology ,business ,Biotechnology - Abstract
Synthetic DNA is becoming an attractive substrate for digital data storage due to its density, durability, and relevance in biological research. A major challenge in making DNA data storage a reality is that reading DNA back into data using sequencing by synthesis remains a laborious, slow and expensive process. Here, we demonstrate successful decoding of 1.67 megabytes of information stored in short fragments of synthetic DNA using a portable nanopore sequencing platform. We design and validate an assembly strategy for DNA storage that drastically increases the throughput of nanopore sequencing. Importantly, this assembly strategy is generalizable to any application that requires nanopore sequencing of small DNA amplicons., A major bottleneck in using DNA as a data storage medium is the slowness of sequencing. Here the authors decode 1.67 megabytes of information using a portable nanopore platform with an assembly strategy for increased throughput.
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- 2019
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11. Nucleic Acid Databases and Molecular-Scale Computing
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Xin Song and John H. Reif
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business.industry ,Computer science ,General Engineering ,General Physics and Astronomy ,DNA ,Sequence Analysis, DNA ,Modular design ,law.invention ,Data recovery ,Computers, Molecular ,Synthetic biology ,Digital Data Storage ,Computer architecture ,DNA computing ,law ,DNA nanotechnology ,Scalability ,Animals ,Humans ,Synthetic Biology ,General Materials Science ,Databases, Nucleic Acid ,business ,Massively parallel - Abstract
DNA outperforms most conventional storage media in terms of information retention time, physical density, and volumetric coding capacity. Advances in synthesis and sequencing technologies have enabled implementations of large synthetic DNA databases with impressive storage capacity and reliable data recovery. Several robust DNA storage architectures featuring random access, error correction, and content rewritability have been constructed with the potential for scalability and cost reduction. We survey these recent achievements and discuss alternative routes for overcoming the hurdles of engineering practical DNA storage systems. We also review recent exciting work on in vivo DNA memory including intracellular recorders constructed by programmable genome editing tools. Besides information storage, DNA could serve as a versatile molecular computing substrate. We highlight several state-of-the-art DNA computing techniques such as strand displacement, localized hybridization chain reactions, and enzymatic reaction networks. We summarize how these simple primitives have facilitated rational designs and implementations of in vitro DNA reaction networks that emulate digital/analog circuits, artificial neural networks, or nonlinear dynamic systems. We envision these modular primitives could be strategically adapted for sophisticated database operations and massively parallel computations on DNA databases. We also highlight in vivo DNA computing modules such as CRISPR logic gates for building scalable genetic circuits in living cells. To conclude, we discuss various implications and challenges of DNA-based storage and computing, and we particularly encourage innovative work on bridging these two areas of research to further explore molecular parallelism and near-data processing. Such integrated molecular systems could lead to far-reaching applications in biocomputing, security, and medicine.
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- 2019
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12. Molecular digital data storage using DNA
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Karin Strauss, Luis Ceze, and Jeff Nivala
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0303 health sciences ,Information storage ,business.industry ,DNA digital data storage ,Biology ,Data science ,Archival research ,03 medical and health sciences ,Digital Data Storage ,chemistry.chemical_compound ,0302 clinical medicine ,Dna genetics ,chemistry ,Computer data storage ,Genetics ,Molecular memory ,business ,Molecular Biology ,030217 neurology & neurosurgery ,Genetics (clinical) ,DNA ,030304 developmental biology - Abstract
Molecular data storage is an attractive alternative for dense and durable information storage, which is sorely needed to deal with the growing gap between information production and the ability to store data. DNA is a clear example of effective archival data storage in molecular form. In this Review, we provide an overview of the process, the state of the art in this area and challenges for mainstream adoption. We also survey the field of in vivo molecular memory systems that record and store information within the DNA of living cells, which, together with in vitro DNA data storage, lie at the growing intersection of computer systems and biotechnology.
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- 2019
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13. Introduction of the ARDS—Anti-Ransomware Defense System Model—Based on the Systematic Review of Worldwide Ransomware Attacks
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Veronika Szücs, Gábor Arányi, and Ákos Dávid
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Technology ,cybersecurity ,Computer science ,Network security ,QH301-705.5 ,QC1-999 ,02 engineering and technology ,Computer security ,computer.software_genre ,System model ,Software ,0202 electrical engineering, electronic engineering, information engineering ,Ransomware ,General Materials Science ,Biology (General) ,Instrumentation ,QD1-999 ,Fluid Flow and Transfer Processes ,Network Access Protection ,business.industry ,Process Chemistry and Technology ,autonomous ARDS model ,Physics ,General Engineering ,Software development ,020206 networking & telecommunications ,Engineering (General). Civil engineering (General) ,Computer Science Applications ,Digital Data Storage ,Chemistry ,ransomware ,020201 artificial intelligence & image processing ,The Internet ,TA1-2040 ,business ,computer - Abstract
We live in a world of digital information communication and digital data storage. Following the development of technology, demands from the user side also pose serious challenges for developers, both in the field of hardware and software development. However, the increasing penetration of the Internet, IoT and digital solutions that have become available in almost every segment of life, carries risks as well as benefits. In this study, the authors present the phenomenon of ransomware attacks that appear on a daily basis, which endangers the operation and security of the digital sphere of both small and large enterprises and individuals. An overview of ransomware attacks, the tendency and characteristics of the attacks, which have caused serious financial loss and other damages to the victims, are presented. This manuscript also provides a brief overview of protection against ransomware attacks and the software and hardware options that enhance general user security and their effectiveness as standalone applications. The authors present the results of the study, which aimed to explore how the available software and hardware devices can implement digital user security. Based on the results of the research, the authors propose a complex system that can be used to increase the efficiency of network protection and OS protection tools already available to improve network security, and to detect ransomware attacks early. As a result, the model of the proposed protection system is presented, and it can be stated that the complex system should be able to detect ransomware attacks from either the Internet or the internal network at an early stage, mitigate malicious processes and maintain data in recoverable state.
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- 2021
14. Archives in DNA: Workshop exploring implications of an emerging bio-digital technology through design fiction
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Stefan Poslad, Chang Hee Lee, Raphael Kim, Larissa Pschetz, and Conor Linehan
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Data ,Emerging technologies ,High density ,Design fiction ,Archive ,DNA ,Data science ,Commercialization ,Bio-digital ,Digital Data Storage ,Speculative design ,Political science ,Production (economics) ,Sociocultural evolution ,Futures contract - Abstract
Continuing developments in DNA-based digital data storage systems promise us a sustainable, techno-utopian future; propositioning bio-digital solutions addressing the ever-increasing global data production, and inadequacies of conventional storage infrastructure to meet the demand. Distinct attributes of DNA make it an attractive archival medium. With its ability to retain high density of digital information cheaply, and to do so over multi-lifespans, DNA-based storage systems are seen as able to radically shape how we archive and use data, across wide-ranging applications. However, while the stakeholders continue to refine and race towards commercialization of the emerging technology, its sociocultural and ethical implications remain unexplored, limiting opportunities to generate insights on how such systems could be better designed and experienced. This workshop begins to explore what our DNA-mediated archival futures may hold. We learn about the fundamental principles governing the new technology and create stories about its pervasion in our lives, mediated through design fiction and structured discourse.
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- 2021
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15. Self-replicating digital data storage with synthetic chromosomes
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Tom Ellis and Xinyu Lu
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Digital Data Storage ,Multidisciplinary ,AcademicSubjects/SCI00010 ,Computer science ,business.industry ,RESEARCH HIGHLIGHT ,AcademicSubjects/MED00010 ,business ,Information Science ,Computer hardware - Published
- 2021
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16. Error-Free Synthetic DNA by Molecular Dictation
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Laurens Lindenburg, Philipp Knyphausen, Florian Hollfelder, Hollfelder, Florian [0000-0002-1367-6312], and Apollo - University of Cambridge Repository
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0301 basic medicine ,error correction ,Computer science ,Information Storage and Retrieval ,Bioengineering ,02 engineering and technology ,Computational biology ,03 medical and health sciences ,chemistry.chemical_compound ,Synthetic biology ,Synthetic DNA ,Throughput (business) ,DNA synthesis ,Dictation ,High-Throughput Nucleotide Sequencing ,DNA ,021001 nanoscience & nanotechnology ,Digital Data Storage ,030104 developmental biology ,chemistry ,synthetic biology ,0210 nano-technology ,Error detection and correction ,Biotechnology - Abstract
Synthetic DNA is the linchpin of the rapidly accelerating biotechnological era and is perhaps the most promising candidate for long-term digital data storage. Despite huge advances, manufacturing error-free DNA at low cost and high throughput remains challenging. Borrowing from well-established sequencing-by-synthesis technologies, we describe a new solution for DNA error correction.
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- 2021
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17. Virtual Manager for Medical Practitioners
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Sakshi Khose, Sonal Sarode, Varad More, and Smita Rukhande
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Named entity ,World Wide Web ,Digital Data Storage ,File management ,Computer science ,Perception ,media_common.quotation_subject ,Conversation ,Medical prescription ,Health records ,Remote assistance ,media_common - Abstract
The rise of Artificial Intelligence(AI) and Natural Language Processing (NLP) gave a perception of the use of computers in the Healthcare industry. The introduction of voice-assisted chatbots and digital data storage aided health organizations as well as the dependents. Currently, the interactions between doctors and patients are undocumented, and the prescription, in some cases, creates chaos for understanding and long-term maintenance. The project introduces an interactive virtual assistant system for searching, analyzing, and recording clinical data and laboratory data, maintaining electronic health records. It uses a Named Entity Extraction (NER) model for classifying the doctor-patient conversation, i.e., symptoms, detected disorder, prescription of drugs, and stores them in a Structured database. The system poses an ability to understand and respond to limited user queries and imitate human discourse to stimulate a conversation that resembles conversing with a real person. The response includes the recorded history of patients, overcoming the issue of file management, supporting clinical decisions. Generates automated prescriptions eliminating the problems of handwritten prescriptions, and provides live news updates with the web scraper module. Moreover, it plays a vital role in reminding patients about their deadlines for vaccinations and follow-ups.
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- 2021
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18. Scaling up DNA digital data storage by efficiently predicting DNA hybridisation using deep learning
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David Buterez and Apollo - University of Cambridge Repository
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FOS: Computer and information sciences ,Computer Science - Machine Learning ,Computer science ,Science ,Distributed computing ,Information Storage and Retrieval ,Quantitative Biology - Quantitative Methods ,Article ,law.invention ,Machine Learning (cs.LG) ,Reduction (complexity) ,Computers, Molecular ,Deep Learning ,DNA computing ,law ,Computational platforms and environments ,Machine learning ,Hardware and infrastructure ,Throughput (business) ,Quantitative Methods (q-bio.QM) ,Multidisciplinary ,business.industry ,Deep learning ,Nucleic Acid Hybridization ,Data processing ,Digital Data Storage ,Workflow ,Data point ,FOS: Biological sciences ,Scalability ,Medicine ,Artificial intelligence ,business - Abstract
Deoxyribonucleic acid (DNA) has shown great promise in enabling computational applications, most notably in the fields of DNA digital data storage and DNA computing. Information is encoded as DNA strands, which will naturally bind in solution, thus enabling search and pattern-matching capabilities. Being able to control and predict the process of DNA hybridisation is crucial for the ambitious future of Hybrid Molecular-Electronic Computing. Current tools are, however, limited in terms of throughput and applicability to large-scale problems. We present the first comprehensive study of machine learning methods applied to the task of predicting DNA hybridisation. For this purpose, we introduce an in silico-generated hybridisation dataset of over 2.5 million data points, enabling the use of deep learning. Depending on hardware, we achieve a reduction in inference time ranging from one to over two orders of magnitude compared to the state-of-the-art, while retaining high fidelity. We then discuss the integration of our methods in modern, scalable workflows., Comment: 30 pages, 6 figures (including 13 pages of supplementary information and 2 supplementary figures)
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- 2021
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19. Value-Added Process Design for Digital Transformation in Hospitals and Medical Networks
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Ralf-Joachim Schulz and Martin Schönheit
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Value (ethics) ,Digital Data Storage ,Documentation ,Risk analysis (engineering) ,Data exchange ,business.industry ,Computer science ,Digital transformation ,Pharmacy ,Process design ,Medical diagnosis ,business - Abstract
The practical possibilities of medical diagnostics and care have improved dramatically in recent years. This has been made possible by the latest diagnostics and therapeutic approaches, which can be implemented into old age. This has resulted in a wealth of information that is only possible with the help of digital data storage and data transfer to cooperating partners. In the last 10 years, the urgent need for care networks with joint treatment concepts and data exchange has arisen on this basis. The growing group of elderly, multimorbid patients poses a particular challenge. On average, these patients have 12 diagnoses and make use of a large number of co-treating medical colleagues. But also nursing and pharmacy documentation must be available in real time. The challenge of the future will be to have this information available at all times and to be able to interpret a patient’s medical situation in real time. The challenge also lies in the fact that there is an increasing shortage of personnel in the nursing and medical services, so that new monitoring devices are being sought to integrate information into this trans-sectoral data network. The article points out to partners and possible solutions currently emerging in the health market.
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- 2021
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20. An Empirical Comparison of Preservation Methods for Synthetic DNA Data Storage
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A. Xavier Kohll, Lee Organick, Rachel McAmis, Weida D. Chen, Siena Dumas Ang, Luis Ceze, Karin Strauss, Robert N. Grass, and Bichlien H. Nguyen
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Time Factors ,Computer science ,DNA digital data storage ,Computational biology ,Stability (probability) ,Polymerase Chain Reaction ,DNA sequencing ,chemistry.chemical_compound ,Synthetic DNA ,General Materials Science ,Magnetite Nanoparticles ,Base Sequence ,business.industry ,Temperature ,High-Throughput Nucleotide Sequencing ,Trehalose ,General Chemistry ,DNA ,Sequence Analysis, DNA ,Accelerated aging ,Digital Data Storage ,chemistry ,Computer data storage ,business ,Half-Life - Abstract
Synthetic DNA has recently risen as a viable alternative for long‐term digital data storage. To ensure that information is safely recovered after storage, it is essential to appropriately preserve the physical DNA molecules encoding the data. While preservation of biological DNA has been studied previously, synthetic DNA differs in that it is typically much shorter in length, it has different sequence profiles with fewer, if any, repeats (or homopolymers), and it has different contaminants. In this paper, nine different methods used to preserve data files encoded in synthetic DNA are evaluated by accelerated aging of nearly 29 000 DNA sequences. In addition to a molecular count comparison, the DNA is also sequenced and analyzed after aging. These findings show that errors and erasures are stochastic and show no practical distribution difference between preservation methods. Finally, the physical density of these methods is compared and a stability versus density trade‐offs discussion provided.
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- 2020
21. Keyword-Based Hadith Grouping Using Fuzzy C-Means Method
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N. Nelis Febriani Sm, Evi Dewi Sri Mulyani, Dani Rohpandi, Rahadi Deli Saputra, Adam Darmawan, and Restu Adi Wiyono
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Digital Data Storage ,Software ,Information retrieval ,business.industry ,Computer science ,ComputingMethodologies_DOCUMENTANDTEXTPROCESSING ,business ,Computer-aided software engineering ,Cluster analysis ,Fuzzy logic - Abstract
Most of the Islamic documents have been documented and published to Muslims to be studied and applied in daily activities. One of these documents is a Hadith. Along with the development of hadith technology not only recorded on sheets of paper but also stored on digital data storage media in the form of databases. Document grouping allows users to get better information than using documents in the same group. Fuzzy techniques allow different membership levels. The purpose of grouping documents is to get different groups. This is needed for better document search. The document used in this study is an Indonesian translation of the Sunnan An Nasa'i Hadith tradition with a grouping technique using a combination of Text Mining and Fuzzy C-Means algorithm as a method of grouping it. By comparing the results of manual calculations against the results of calculations using RStudio software, the accuracy obtained is 80%.
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- 2020
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22. Photon-directed multiplexed enzymatic DNA synthesis for molecular digital data storage
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Daniel J. Wiegand, Honggu Chun, Sukanya Punthambaker, George M. Church, Howon Lee, Kettner Griswold, and Richie E. Kohman
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0301 basic medicine ,Ultraviolet Rays ,Science ,Oligonucleotides ,Information Storage and Retrieval ,General Physics and Astronomy ,Nanotechnology ,Multiplexing ,Chemical synthesis ,Article ,General Biochemistry, Genetics and Molecular Biology ,DNA sequencing ,law.invention ,03 medical and health sciences ,chemistry.chemical_compound ,Synthetic biology ,law ,DNA Nucleotidylexotransferase ,lcsh:Science ,Video game ,Oligonucleotide Array Sequence Analysis ,Multidisciplinary ,030102 biochemistry & molecular biology ,DNA synthesis ,Oligonucleotide ,DNA ,General Chemistry ,Digital Data Storage ,030104 developmental biology ,chemistry ,DNA and RNA ,lcsh:Q ,Photolithography - Abstract
New storage technologies are needed to keep up with the global demands of data generation. DNA is an ideal storage medium due to its stability, information density and ease-of-readout with advanced sequencing techniques. However, progress in writing DNA is stifled by the continued reliance on chemical synthesis methods. The enzymatic synthesis of DNA is a promising alternative, but thus far has not been well demonstrated in a parallelized manner. Here, we report a multiplexed enzymatic DNA synthesis method using maskless photolithography. Rapid uncaging of Co2+ ions by patterned UV light activates Terminal deoxynucleotidyl Transferase (TdT) for spatially-selective synthesis on an array surface. Spontaneous quenching of reactions by the diffusion of excess caging molecules confines synthesis to light patterns and controls the extension length. We show that our multiplexed synthesis method can be used to store digital data by encoding 12 unique DNA oligonucleotide sequences with video game music, which is equivalent to 84 trits or 110 bits of data., Writing data in DNA is still a bottleneck due to the reliance on chemical synthesis methods. Here the authors report multiplexed enzymatic DNA synthesis using maskless photolithography.
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- 2020
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23. A quaternary code mapping resistant to the sequencing noise for DNA image coding
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Marc Antonini, Melpomeni Dimopoulou, Eva Gil San Antonio, Laboratoire d'Informatique, Signaux, et Systèmes de Sophia-Antipolis (I3S) / Projet MEDIACODING, Signal, Images et Systèmes (Laboratoire I3S - SIS), Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)
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0303 health sciences ,business.industry ,Computer science ,Noise (signal processing) ,Reading (computer) ,020206 networking & telecommunications ,02 engineering and technology ,computer.software_genre ,DNA sequencing ,03 medical and health sciences ,Digital Data Storage ,[INFO.INFO-TS]Computer Science [cs]/Signal and Image Processing ,[INFO.INFO-IT]Computer Science [cs]/Information Theory [cs.IT] ,Computer data storage ,0202 electrical engineering, electronic engineering, information engineering ,Code (cryptography) ,Redundancy (engineering) ,[INFO]Computer Science [cs] ,Data mining ,Error detection and correction ,business ,computer ,030304 developmental biology - Abstract
International audience; The exponential growth in the generation of digital information creates a big challenge for data storage given the capacity limitations of conventional storage devices. Recent works have proposed DNA as a means of digital data storage proposing a novel solution for long-term storage. Although having many advantages, DNA storage is a challenging topic due to the error-prone process of DNA sequencing (reading). To deal with this error most existing works focus on the introduction of error-correction methods. However, most of those methods introduce important redundancy without promising full error correction for the widely used sequencing method using the Nanopore sequencer. This work focuses on noise resistance rather than error-correction proposing a new algorithm for optimally assigning VQ indices to DNA codewords while reducing the visual impact of substitution errors that are caused during sequencing.
- Published
- 2020
24. DNA Data Storage and Hybrid Molecular–Electronic Computing
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Georg Seelig, Douglas Carmean, Karin Strauss, Max Willsey, Kendall Stewart, and Luis Ceze
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Digital Data Storage ,Computer architecture ,Computer science ,Emerging technologies ,business.industry ,Encoding (memory) ,DNA digital data storage ,Pipeline (computing) ,System integration ,Electrical and Electronic Engineering ,Architecture ,business ,Massively parallel - Abstract
Moore’s law may be slowing, but our ability to manipulate molecules is improving faster than ever. DNA could provide alternative substrates for computing and storage as existing ones approach physical limits. In this paper, we explore the implications of this trend in computer architecture. We present a computer systems perspective on molecular processing and storage, positing a hybrid molecular–electronic architecture that plays to the strengths of both domains. We cover the design and implementation of all stages of the pipeline: encoding, DNA synthesis, system integration with digital microfluidics, DNA sequencing (including emerging technologies such as nanopores), and decoding. We first draw on our experience designing a DNA-based archival storage system, which includes the largest demonstration to date of DNA digital data storage of over three billion nucleotides encoding over 400 MB of data. We then propose a more ambitious hybrid–electronic design that uses a molecular form of near-data processing for massive parallelism. We present a model that demonstrates the feasibility of these systems in the near future. We think the time is ripe to consider molecular storage seriously and explore system designs and architectural implications.
- Published
- 2019
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25. Efficient Storage of Images onto DNA using Vector Quantization
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Marc Antonini, Melpomeni Dimopoulou, Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Laboratoire d'Informatique, Signaux, et Systèmes de Sophia-Antipolis (I3S) / Equipe IMAGES-CREATIVE, Signal, Images et Systèmes (Laboratoire I3S - SIS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S)
- Subjects
business.industry ,Computer science ,DNA digital data storage ,Digital data ,Vector quantization ,Optical storage ,Digital Data Storage ,Workflow ,[INFO.INFO-TS]Computer Science [cs]/Signal and Image Processing ,Encoding (memory) ,[INFO]Computer Science [cs] ,business ,Computer hardware ,Image compression - Abstract
International audience; The archiving of digital data is becoming very challenging as conventional electronic devices wear out in time leaving at stake any data that has been stored in them. Therefore, data migration is necessary every 5-10 years. Unfortunately, the maintenance and replacement of servers in big data centers is very expensive both in terms of money and energy. DNA data storage is a new evolving technique which proposes an efficient and eco-friendly solution while also promising data longevity due to the use of DNA as a means of digital data storage. Storing digital information into DNA is feasible by encoding it in a quaternary representation using the four DNA nucleotides (nts) A, T, C and G which is later going to be synthesized into DNA. Then, thanks to some machines which are called sequencers, one can read back the synthetic DNA and retrieve the corresponding quaternary sequence. Finally, using a decoding procedure the stored data can be recovered. The most challenging part of this procedure is the fact that the reading process of sequencing is error-prone. Respecting some special restrictions in the encoding can lead to a more reliable reconstruction. More precisely the existence of homopolymers, a high percentage of G and C or the repetition of short patterns in the encoded sequence can lead to high se-quencing error. Furthermore, as DNA synthesis costs several dollars per DNA strand (200 nts), it is also important to ensure that the encoding is efficient in terms of data compression. Consequently the selection of an appropriate encoding algorithm is highly important. In this work we propose a new end-to-end encoding schema which is specific for the efficient storage of images onto synthetic DNA. This algorithm uses a DWT to create wavelet sub-bands and then quantizes each one of them using a Vector Quantizer(VQ). Quantization is optimized by a source allocation algorithm which allows selection of an optimal number of vectors and an optimal length of vectors that provide the minimum distortion at a given rate. The optimally compressed sub-band coefficients are then encoded into a sequence of A, T, C, G using a robust algorithm which respects the restrictions imposed by the biological procedure of DNA sequencing to ensure reliability of the decoding. The novelty of this work compared to the existing state of the art lies in the implementation of a full encoding workflow which minimizes the cost of storing images into DNA while avoiding the creation of patterns which can occur when using VQ. Our results show great improvement in the rate-distortion curve from our previous experiments that have been using uniform quantization while also producing DNA strands which respect all the necessary sequencing restrictions. More precisely VQ allows us to improve the coding rate to 3.34 bits/nt which is a very good performance compared to the state of the art.
- Published
- 2020
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26. DNA Micro-Disks for the Management of DNA-Based Data Storage with Index and Write-Once-Read-Many (WORM) Memory Features
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Jinwoo Hyun, H.C. Kim, Taehoon Ryu, Hansol Choi, Seojoo Kim, Kibeom Kim, Amos Chungwon Lee, Wook Park, Daewon Lee, Suk-Heung Song, Sunghoon Kwon, Yeongjae Choi, and Hyung Jong Bae
- Subjects
Materials science ,Library ,Computer science ,Reliability (computer networking) ,Information Storage and Retrieval ,02 engineering and technology ,Data loss ,010402 general chemistry ,01 natural sciences ,chemistry.chemical_compound ,Write once read many ,Data_FILES ,General Materials Science ,Computer Storage Devices ,business.industry ,Mechanical Engineering ,Search engine indexing ,DNA ,021001 nanoscience & nanotechnology ,0104 chemical sciences ,Digital Data Storage ,chemistry ,Mechanics of Materials ,Embedded system ,Data quality ,Computer data storage ,0210 nano-technology ,business - Abstract
DNA-based data storage has attracted attention because of its higher physical density of the data and longer retention time than those of conventional digital data storage1–7. However, previous DNA-based data storage lacked index features and the data quality of storage after a single access is not preserved, obstructing its industrial use. Here, we propose DNA micro-disks, quick response (QR)-coded micro-sized disks that harbour data-encoded DNA molecules for the efficient management of DNA-based data storage. We demonstrate the two major features that previous DNA-based data storage studies could not achieve. One feature is accessing data items efficiently by indexing the data-encoded DNA library. Another is achieving write-once-read-many (WORM) memory through the immobilization of DNA molecules on the disk and their enrichment through in situ DNA production. Through these features, the reliability of DNA-based data storage was increased by allowing multiple accession of data-encoded DNA without data loss.
- Published
- 2020
27. New Trends in Digital Data Storage for the Internet of Things
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A. Saxena, A. Sharma, C. Patel, S. Dangi, and S. Sharma
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World Wide Web ,Digital Data Storage ,business.industry ,Computer science ,Internet of Things ,business - Published
- 2018
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28. The intensive use of digital data in modern natural science
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G. A. Kobzev, A. O. Erkimbaev, and V. Yu. Zitserman
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Class (computer programming) ,Data curation ,Computer science ,05 social sciences ,Digital data ,Sample (statistics) ,050905 science studies ,Data science ,Data set ,Metadata ,Digital Data Storage ,Annotation ,0509 other social sciences ,050904 information & library sciences ,General Economics, Econometrics and Finance - Abstract
Common approaches and technologies applied to digital data storage and processing in various disciplines are analyzed. It is shown that regardless of a specific subject area, working with large data set obtained as a result of experimenting or modeling requires similar methodological support, involving data curation, metadata support, and data genesis and quality annotation. The interdisciplinary field called “The properties of materials and substances” is analyzed as an example of a discipline that actively applies digital data. New approaches to the integration of data with heterogeneous properties that take into account structural data variations by the class of substances, the state of sample, experimental conditions, and other factors are investigated.
- Published
- 2017
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29. DNA as Digital Data Storage: Opportunities and Challenges for HCI
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Raphael Kim
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Information management ,business.industry ,Computer science ,media_common.quotation_subject ,05 social sciences ,020207 software engineering ,Context (language use) ,02 engineering and technology ,Data science ,Digital Data Storage ,User experience design ,Computer data storage ,0202 electrical engineering, electronic engineering, information engineering ,Key (cryptography) ,0501 psychology and cognitive sciences ,Product (category theory) ,business ,Function (engineering) ,050107 human factors ,media_common - Abstract
DNA molecules can retain information in high densities, with high durability and low overall energy cost. This would make DNA-based data storage system a compelling solution in placating the increasing gap between global data production and our current means to store data. While key technical developments in recent decades have allowed DNA-based data storage systems to slowly progress closer to mainstream usage, there has been an overall lack of discourse surrounding potential implications of the system in the context of human computer interaction (HCI). This article introduces the DNA-based technology, followed by highlights of some of the potential opportunities and challenges it brings to the HCI community. In summary, DNA-based data storage systems offer a new research topic for user experience studies and data physicalization, and these are driven by inherent biological qualities of the DNA. As a tool, given the longevity of DNA, the system could also function as a multi-lifespan information management product, designed to help in addressing long-term wicked problems. In terms of challenges, ethical implications surrounding the technology ownership, and communication hurdles for HCI researchers working with the new technology, should also be considered and addressed.
- Published
- 2020
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30. Aerolysin nanopores decode digital information stored in tailored macromolecular analytes
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Chan Cao, Jean-François Lutz, Niklas Felix König, Lucien Krapp, Abdelaziz Al Ouahabi, Matteo Dal Peraro, Nuria Cirauqui, Aleksandra Radenovic, Ecole Polytechnique Fédérale de Lausanne (EPFL), Institut Charles Sadron (ICS), Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et Nanosciences Grand-Est (MNGE), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Lutz, Jean-François, Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Matériaux et nanosciences d'Alsace (FMNGE), and Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
[CHIM.POLY] Chemical Sciences/Polymers ,Computer science ,Big data ,Digital data ,Biophysics ,Aerolysin ,Nanotechnology ,Cryptography ,010402 general chemistry ,01 natural sciences ,03 medical and health sciences ,Research Articles ,030304 developmental biology ,0303 health sciences ,Chemical Physics ,Multidisciplinary ,business.industry ,Process (computing) ,SciAdv r-articles ,0104 chemical sciences ,Digital Data Storage ,Nanopore ,[CHIM.POLY]Chemical Sciences/Polymers ,Computer data storage ,business ,Research Article - Abstract
Informational polymers are deciphered by aerolysin pores., Digital data storage is a growing need for our society and finding alternative solutions than those based on silicon or magnetic tapes is a challenge in the era of “big data.” The recent development of polymers that can store information at the molecular level has opened up new opportunities for ultrahigh density data storage, long-term archival, anticounterfeiting systems, and molecular cryptography. However, synthetic informational polymers are so far only deciphered by tandem mass spectrometry. In comparison, nanopore technology can be faster, cheaper, nondestructive and provide detection at the single-molecule level; moreover, it can be massively parallelized and miniaturized in portable devices. Here, we demonstrate the ability of engineered aerolysin nanopores to accurately read, with single-bit resolution, the digital information encoded in tailored informational polymers alone and in mixed samples, without compromising information density. These findings open promising possibilities to develop writing-reading technologies to process digital data using a biological-inspired platform.
- Published
- 2020
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31. Secure data storage on DNA hard drives
- Author
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Ulrich F. Keyser, Filip Bošković, Kaikai Chen, and Jinbo Zhu
- Subjects
0303 health sciences ,business.industry ,Base pair ,Oligonucleotide ,Computer science ,Data security ,02 engineering and technology ,021001 nanoscience & nanotechnology ,Encryption ,Dna storage ,03 medical and health sciences ,chemistry.chemical_compound ,Nanopore ,Digital Data Storage ,chemistry ,Encoding (memory) ,Computer data storage ,Key (cryptography) ,0210 nano-technology ,business ,Computer hardware ,Decoding methods ,DNA ,030304 developmental biology - Abstract
DNA is emerging as a novel material for digital data storage. The two main challenges are efficient encoding and data security. Here, we develop an approach that allows for writing and erasing data by relying solely on Watson-Crick base pairing of short oligonucleotides to single-stranded DNA overhangs located along a long double-stranded DNA hard drive (DNA-HD). Our enzyme-free system enables fast synthesis-free data writing with predetermined building blocks. The use of DNA base pairing allows for secure encryption on DNA-HDs that requires a physical key and nanopore sensing for decoding. The system is suitable for miniature integration for an end-to-end DNA storage device. Our study opens a novel pathway for rewritable and secure data storage with DNA.One Sentence SummaryStoring digital information on molecules along DNA hard drives for rewritable and secure data storage.
- Published
- 2019
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32. Photo Annotation: A Study on Automatic Photo Management Based on Contextual Information
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Umma Habiba and Md. Alvee Noor
- Subjects
Information retrieval ,Event (computing) ,Computer science ,ComputingMethodologies_IMAGEPROCESSINGANDCOMPUTERVISION ,Process (computing) ,020206 networking & telecommunications ,020207 software engineering ,02 engineering and technology ,Metadata ,Annotation ,Digital Data Storage ,0202 electrical engineering, electronic engineering, information engineering ,Contextual information ,Daylight ,Photo management - Abstract
The increasing number of photos that people keep in their digital data storage devices often get scattered and it gets quite difficult to keep track of them effectively in time of need or to manage them efficiently. We present a process of photo annotation based on the metadata of the images and have developed a photo management application that derives information of location, daylight, weather, event name and persons related to the photo through external application programming interfaces (API) and libraries from the respective images metadata. These informations are annotated against the photos and saved into the database of the application so that the photos can be brought into the users view when they are sought according to these informations i.e. the location or event on which a particular photo was taken. We have also created a test database of 1350 images and our application has the accuracy of 82% for Daylight, 27.85% for events, 95% for locations, 40.75% for persons and 80% for weather data. The test images are taken from a span of two years and are of 40 events, 45 locations and of 25 camera models.
- Published
- 2019
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- View/download PDF
33. Topography measurement of glass disk substrates with sub-nanometer resolution
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Chris L. Koliopoulos and Klaus Freischlad
- Subjects
Interferometry ,Digital Data Storage ,Materials science ,Optics ,Waviness ,business.industry ,Surface metrology ,Speckle noise ,Wafer ,business ,Axial symmetry ,Coherence (physics) - Abstract
With their high capacity and low cost, magnetic disks remain competitive for digital data storage. The low flying heights of the read/write head in the single nm-range place stringent requirements on the disk substrate topography. Interferometric surface metrology can provide the required topography data. For the measurement of state-of-the-art disk substrates with Angstrom-level waviness, the interferometer noise needs to be extremely low. A robust and cost-effective approach uses an LED as a light source providing temporally and spatially low-coherence illumination. The low temporal coherence leads to axially localized fringes, and clean single-surface fringes and topography maps are obtained even for transparent substrates. The low spatial coherence suppresses coherent noise, or speckle noise, in the fringe intensities and topography maps. Coherent noise cannot be determined by a simple repeatability measurement, since it is stable over some time for a given disk alignment. It does not appear in difference maps, but nevertheless is present in all acquired maps. An upper limit of low-level coherent noise is determined by looking at speckle decorrelation with increasing tilt of the test surface. In this presentation, the coherence issues are discussed together with the characterization of coherent noise and waviness filtering. Disk measurement examples are shown where the data were acquired with OptoFlat, an LED-based interferometer newly developed for the measurement of flat surfaces like disks and wafers.
- Published
- 2019
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34. Deoxyribonucleic Acid (DNA): The Magician in the Field of the Digital Data Storage
- Author
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Jun He, David H. Coy, Lichun Sun, and Jing Luo
- Subjects
chemistry.chemical_compound ,Digital Data Storage ,Data encoding ,Field (physics) ,Biochemistry ,Chemistry ,Guanine ,Replication (statistics) ,General Medicine ,DNA ,Thymine - Published
- 2019
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35. DNA Digital Data Storage based on Distributed Method
- Author
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Yang Zhang, Yi Zhao, and Yu Wang
- Subjects
0301 basic medicine ,business.industry ,Computer science ,Distributed element model ,010401 analytical chemistry ,Word error rate ,Coding theory ,computer.file_format ,Storage tube ,01 natural sciences ,Storage model ,0104 chemical sciences ,Data conversion ,03 medical and health sciences ,Digital Data Storage ,030104 developmental biology ,business ,Error detection and correction ,computer ,Computer hardware - Abstract
DNA digital data storage refers to the technique of storing digital information on synthetic DNA. This paper introduces the method of converting digital information into genetic code based on ternary data conversion method. The "end-to-end" gene storage model was proposed without the use of address bits, which enabling unlimited information storage. With the distributed model, the information is evenly distributed among a plurality of storage tubes. Each storage tube eliminates a certain amount of data according to the congruence misplacement, and each of the chains adds 8-bit error correction bits. As a result, even if the order is disrupted, the regular order of genes can be still recovered by comparing the points. The error rate can be controlled at the average of, and the highest is, which is robust and secure.
- Published
- 2019
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- View/download PDF
36. An Efficient and Secure Forward Error Correcting Scheme for DNA Data Storage
- Author
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Mostafa Belkasmi, Anouar Yatribi, and Fouad Ayoub
- Subjects
0301 basic medicine ,Computer science ,DNA digital data storage ,Search engine indexing ,020206 networking & telecommunications ,02 engineering and technology ,03 medical and health sciences ,Digital Data Storage ,030104 developmental biology ,Header ,Scalability ,0202 electrical engineering, electronic engineering, information engineering ,Error correcting ,Algorithm ,Decoding methods ,Coding (social sciences) - Abstract
In this paper, a new efficient error correcting scheme for DNA archival digital data storage is proposed. We devise a double protection scheme for DNA oligos, aiming to ensure the protection of both information and indexing header data from both symbol flipping and erasure-burst errors, using two different cyclic ternary difference-set codes, which are known to be completely orthogonalisable and very easy to decode using a simple majority-logic decoding algorithm. We show that the proposed scheme is efficient and easily scalable, and provides a coding potential of 1.97 bit per nucleotide, and a reasonable net information density of 0.75 bit/nt under the considered experimental conditions, with relatively a lower decoding complexity and costs compared to other DNA data storage approaches.
- Published
- 2019
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37. Spintronics, Magnetoresistive Heads, and the Emergence of the Digital World
- Author
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Jeffrey R. Childress and Eric E. Fullerton
- Subjects
Digital Data Storage ,Magnetoresistance ,Spintronics ,business.industry ,Digital storage ,Computer science ,Electrical engineering ,Electrical and Electronic Engineering ,business - Abstract
The development of spintronics has had a dramatic impact on the evolution of the magnetic hard disk drive and, in turn, on the ubiquitous nature of digital data in modern society. The advent of the magnetoresistive read head technology transitioning from the anisotropic magnetoresistance read head to the spintronics-based giant-magnetoresistance read head and the tunneling magnetoresistance read head were major drivers in this remarkable increase in digital storage. We will review the development of magnetoresistive read head technologies and their impact on digital data storage. We will then highlight the current state-of-the-art sensor and potential future technologies.
- Published
- 2016
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38. Digital Data Storage on DNA
- Author
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Raunak Laddha and Kishor Honwadkar
- Subjects
0301 basic medicine ,chemistry.chemical_classification ,Computer science ,business.industry ,ComputerApplications_COMPUTERSINOTHERSYSTEMS ,ENCODE ,World Wide Web ,03 medical and health sciences ,Digital Data Storage ,chemistry.chemical_compound ,030104 developmental biology ,chemistry ,Nucleotide ,business ,Computer hardware ,DNA - Abstract
Digital data has changed the use and access of information. Everyday lot of data is produced and this requires highdensity storage devices which can retain values for a long time[1]. Deoxyribonucleic acid (DNA) can be potentially used for these purposes as it is not much different from the conventional method used in a computer. DNA can be used as a robust and high-density storage device even under unfavourable conditions[2]. Theoretically, one can encode 2 bits per nucleotide in DNA which can store 455 exabytes per gram maximum data in single-stranded DNA (ssDNA)[3]. In this paper, the method described can be used to store text data in DNA by compressing, storing multiple copies along with providing security to data. General Terms Storage method and compression.
- Published
- 2016
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39. Forward Error Correction for DNA Data Storage
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Samuel A. Inverso, George M. Church, Xiaoming Chen, Ingo Hütter, Meinolf Blawat, Brian M. Turczyk, Benjamin W. Pruitt, and Klaus Gaedke
- Subjects
0301 basic medicine ,Computer science ,DNA digital data storage ,Bio-technology ,02 engineering and technology ,Residual ,computer.software_genre ,digital data storage ,03 medical and health sciences ,chemistry.chemical_compound ,0202 electrical engineering, electronic engineering, information engineering ,A-DNA ,Forward error correction ,data preservation ,General Environmental Science ,DNA synthesis ,business.industry ,020206 networking & telecommunications ,DNA synthesis and sequencing ,DNA ,Dna storage ,Digital Data Storage ,archiving ,030104 developmental biology ,chemistry ,Computer data storage ,General Earth and Planetary Sciences ,Data mining ,business ,computer ,Computer hardware - Abstract
We report on a strong capacity boost in storing digital data in synthetic DNA. In principle, synthetic DNA is an ideal media to archive digital data for very long times because the achievable data density and longevity outperforms today's digital data storage media by far. On the other hand, neither the synthesis, nor the amplification and the sequencing of DNA strands can be performed error-free today and in the foreseeable future. In order to make synthetic DNA available as digital data storage media, specifically tailored forward error correction schemes have to be applied. For the purpose of realizing a DNA data storage, we have developed an efficient and robust forwarderror-correcting scheme adapted to the DNA channel. We based the design of the needed DNA channel model on data from a proof-of-concept conducted 2012 by a team from the Harvard Medical School [1]. Our forward error correction scheme is able to cope with all error types of today's DNA synthesis, amplification and sequencing processes, e.g. insertion, deletion, and swap errors. In a successful experiment, we were able to store and retrieve error-free 22 MByte of digital data in synthetic DNA recently. The found residual error probability is already in the same order as it is in hard disk drives and can be easily improved further. This proves the feasibility to use synthetic DNA as longterm digital data storage media.
- Published
- 2016
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40. Implementation and Performance Analysis of Private Cloud Using Openstack Swift and Rclone
- Author
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Adri Priadana and Candra Aditama
- Subjects
business.product_category ,Database ,business.industry ,Computer science ,Cloud computing ,Data loss ,Service provider ,computer.software_genre ,Object storage ,Digital Data Storage ,Computer data storage ,Scalability ,Internet access ,business ,computer - Abstract
Many companies need a storage system that can be accessed in real time by all parts of the company. Most digital data storage methods today still use conventional methods where data is stored on an external hard disk or public cloud. Storage with external hard disk media makes accessing data difficult and has the risk of data loss when storage media is damaged. On the other hand, the storage method using public cloud requires an internet connection with large bandwidth requirements and the company still has to spend a budget on renting it. This study aims to design digital data storage methods using a private cloud that can be accessed in real time by all parts of the company without having to spend a budget on hiring a storage media and renting an internet connection with large bandwidth requirements. A private cloud was built using OpenStack Swift as an object storage service provider and Rclone as a cross-platform computer data management application. The results of this study are the creation of a private cloud that runs object storage services using Swift storage objects with relatively light and high scalability to meet the needs of storing data effectively and efficiently. A private cloud-based data storage media with relatively light and high scalability to meet data storage needs. Data storage media that can be accessed easily without having to use an internet connection with large bandwidth requirements.
- Published
- 2019
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41. It's all about the pentiums: The use, manipulation, and storage of digital microscopy imaging data for the biological sciences
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Jessica E. Hornick and Edward H. Hinchcliffe
- Subjects
Quantitative imaging ,Multimedia ,business.industry ,Computer file ,Cell Biology ,Biology ,computer.software_genre ,Imaging data ,Task (project management) ,Digital Data Storage ,Software ,Genetics ,business ,Biological sciences ,computer ,Developmental Biology ,Digital microscopy - Abstract
SUMMARY Digital microscopy has revolutionized quantitative imaging, with binary-encoded computer files serving to capture and store imaging data sets for analysis. With the ever-present use of computers to generate and store imaging data, it becomes increasingly important to understand how these files are created, and how they can be both used and mis-used. This is a particularly important task for the biologist who may have limited background in computer science. Here we discuss some of the basic aspects of digital data storage and use, including file types, storage media, and the choice between commercial and open-source software. Often, open-source software is written by a user or group of users, and then distributed to the scientific community at large. These can be important tools, but there are some hidden costs to this freeware that we will discuss. We will also compare open-source software to commercial imaging software, which is often written for use by non-computer scientists. Mol. Reprod. Dev. 82: 508–517, 2015. © 2014 Wiley Periodicals, Inc.
- Published
- 2014
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42. FFmpeg Technology Based on Media Asset Management System Design
- Author
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Lei Lei Deng
- Subjects
Multimedia ,business.industry ,Computer science ,Media industry ,Information Dissemination ,General Medicine ,Transcoding ,Digital asset management ,Asset (computer security) ,computer.software_genre ,Digital Data Storage ,Key (cryptography) ,Fixed asset ,Asset management ,business ,computer ,Mass media - Abstract
The use of FFmpeg technology, overcome the current media asset management of some defects, better play the role of media assets. In response to various types of video data, audio data, text, pictures, and other media digital data storage, inventory management, query, edit material transcoding, information dissemination, and equipment and fixed assets to conduct a comprehensive management. The results show that, based on the " technology " of mass media resources, is to promote the media industry is the motive power of development, any form of content are the media core assets. The media asset design, solve the media transmission and conversion, the ultimate guarantee of effective and complete data. Keywords Key words: media assets; FFmpeg; transcoding; digital storage
- Published
- 2013
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43. Assessment of Stand-Alone Displays for Time Management in a Creativity-Driven Learning Environment
- Author
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Søren R. Frimodt-Møller
- Subjects
Engineering ,Modality (human–computer interaction) ,Multimedia ,business.industry ,media_common.quotation_subject ,Learning environment ,Workspace ,Plan (drawing) ,Creativity ,computer.software_genre ,Preference ,Digital Data Storage ,Human–computer interaction ,Time management ,business ,computer ,media_common - Abstract
This paper considers the pros and cons of stand-alone displays, analog (e.g. billboards, blackboards, whiteboards, large pieces of paper etc.) as well as digital (e.g. large shared screens, digital whiteboards or similar), as tools for time management processes in a creativity-driven learning environment. A qualitative study was conducted at the Medialogy education at Aalborg University Esbjerg to probe for attitudes towards time management tools in general and towards having these on a stand-alone display in the workspace of students working in groups on joint projects. Results show that students who use a stand-alone display primarily use an analog one, whereas students who use digital collaborative time management tools prefer to access these on their individual laptops. The students who express preference for analog displays emphasize the advantage of being able to switch to a different modality for in-group discussions, as well as the increased awareness of the time plan caused by such a display. While these advantages would also be advantages for a digital, interactive display, the disadvantages of analog displays listed by the students relate to the fragility of these displays compared to storing information digitally. The findings could indicate a possible market for stand-alone, interactive digital displays combining the ‘touch and feel’ character of an analog board with the convenience of digital data storage.
- Published
- 2017
- Full Text
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44. Bilingual keyword indexing and searching framework
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Kanika, Hemant Darbari, Srishti Gupta, Shashi Pal Singh, and Ajai Kumar
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File system ,Information retrieval ,Database ,Relational database ,Computer science ,business.industry ,05 social sciences ,Search engine indexing ,Big data ,050905 science studies ,computer.software_genre ,File format ,Digital Data Storage ,Computer data storage ,Scalability ,Data_FILES ,0509 other social sciences ,050904 information & library sciences ,business ,computer - Abstract
The rapid growth of digital data storage of medical or health, social media, education and many more in the world has amplified the demand for big data storage, which requires trillion of files having exabytes of data. This growth in data has put up the key question of how we can effectively manage and find the data in the emergent ocean of information. The upcoming demand for data storage in petabytes and exabytes of data has also resulted in putting pressure in organizing the file structure in such a way that retrieval results of searching a keyword should match with the growing pace of data storage. As a result, there is an increase in demand for keyword indexing and searching of file systems. Directly implementing searching methodology in file system has resulted in inefficient and inconsistent results. General purpose indexes may not be suitable for file system searching as it relies on relational databases and may limit the scalability and performance. This proposed bilingual framework for English and Hindi addresses these problems through a novel approach for indexing and searching queries in large scale file system.
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- 2016
- Full Text
- View/download PDF
45. I know what you did last summer... an investigation into remnant data on USB storage devices sold in Australia in 2015
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Nikki Robins, Krishnun Sansurooah, and Patricia A. H. Williams
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Engineering ,020205 medical informatics ,business.industry ,Digital forensics ,02 engineering and technology ,USB ,Terabyte ,Computer security ,computer.software_genre ,Flash memory ,law.invention ,Digital Data Storage ,law ,020204 information systems ,0202 electrical engineering, electronic engineering, information engineering ,Confidentiality ,Electronics ,Privacy law ,business ,computer - Abstract
The demand for portable digital data storage has increased with the evolution and advancement in consumer electronic devices. USB storage devices, also referred to as USB sticks, pen drives, flash drives, thumb drives, and key drives, have replaced many other portable storage. With the evolution of these devices, an increased use for data transportation has been seen for both private and commercial data. USB storage capacity has increased during the past decades with capacities up to one terabyte available today. Such devices are increasingly popular given their robustness, low power consumption, rapid response rates, non-volatile nature, and ease of transportation. This study obtained second hand USB flash memory storage devices, purchased from eBay Australia over a period of seven months, to determine whether there were any traces of data on the devices, and whether or not an attempt had been made to securely wipe the devices. If data fragments were recovered, it was assessed to see if there was a sufficient volume and sensitivity of data to be of value to anyone with malicious intent. The findings from the research show that in the majority of the cases, the USB flash memory storage devices retained a large volume of data. Concurring with outcomes from previous studies in 2009 and 2011, the devices investigated in this study, owned by both individuals and organisations, were used to store highly sensitive and confidential data. This data was not permanently nor securely destroyed prior to disposal (by sale) of the devices. Such incidents highlight the failure to meet regulatory obligations with regard to privacy legislation in Australia.
- Published
- 2016
- Full Text
- View/download PDF
46. Rewritable digital data storage in live cells via engineered control of recombination directionality
- Author
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Jerome Bonnet, Pakpoom Subsoontorn, and Drew Endy
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Recombination, Genetic ,Genetics ,Multidisciplinary ,Integrases ,biology ,business.industry ,Information Storage and Retrieval ,Computational biology ,Biological Sciences ,Flow Cytometry ,Models, Biological ,Integrase ,Synthetic biology ,Digital Data Storage ,Computer data storage ,Escherichia coli ,Recombinase ,biology.protein ,Directionality ,Synthetic Biology ,Excisionase ,Genetic Engineering ,business ,Reprogramming ,Plasmids - Abstract
The use of synthetic biological systems in research, healthcare, and manufacturing often requires autonomous history-dependent behavior and therefore some form of engineered biological memory. For example, the study or reprogramming of aging, cancer, or development would benefit from genetically encoded counters capable of recording up to several hundred cell division or differentiation events. Although genetic material itself provides a natural data storage medium, tools that allow researchers to reliably and reversibly write information to DNA in vivo are lacking. Here, we demonstrate a rewriteable recombinase addressable data (RAD) module that reliably stores digital information within a chromosome. RAD modules use serine integrase and excisionase functions adapted from bacteriophage to invert and restore specific DNA sequences. Our core RAD memory element is capable of passive information storage in the absence of heterologous gene expression for over 100 cell divisions and can be switched repeatedly without performance degradation, as is required to support combinatorial data storage. We also demonstrate how programmed stochasticity in RAD system performance arising from bidirectional recombination can be achieved and tuned by varying the synthesis and degradation rates of recombinase proteins. The serine recombinase functions used here do not require cell-specific cofactors and should be useful in extending computing and control methods to the study and engineering of many biological systems.
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- 2012
- Full Text
- View/download PDF
47. Realistic Life-Cycle Cost Analysis with Typical Sequential Patterns of Pavement Treatment through Association Analysis
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David Jeong and Saeed Abdollahi Pour
- Subjects
Strategic planning ,Engineering ,Data collection ,Operations research ,business.industry ,Mechanical Engineering ,Data set ,Transport engineering ,Life-cycle cost analysis ,Digital Data Storage ,State highway ,Cost analysis ,State (computer science) ,business ,Civil and Structural Engineering - Abstract
Advancements in data collection, digital data storage, and database management technologies have dramatically increased the capabilities of state highway agencies to generate and to store highway project data. The Oklahoma Department of Transportation (DOT), along with other state DOTs, stores a large amount of highway project data throughout the life cycle of highway projects. Although much of the budget is allocated to collecting and maintaining pavement data sets, the amount of benefit from extracting information and knowledge from the data is limited. This study applies association analysis in data mining to the historical treatment data set available in the Oklahoma DOT to identify the typical sequential patterns of treatment activities. Then, a realistic life-cycle cost analysis (LCCA) model based on typical sequential patterns of pavement treatment activities is developed and compared with the traditional LCCA performed by RealCost through an example. The case study indicates that the results of the realistic LCCA can be significantly different from those of the traditional approach. Because life-cycle cost models developed in this study are based on the actual treatment strategies performed by the Oklahoma DOT, it is expected that the life-cycle cost is closer to actual costs than the traditional approach. Using the realistic LCCA model developed in this study, state DOTs will be able to develop more realistic pavement maintenance and rehabilitation strategies and budgets.
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- 2012
- Full Text
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48. A Two-Dimensional Channel Model for Digital Data Storage on Microfilm
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T. Fingscheidt and C. Voges
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Engineering ,business.industry ,Noise (signal processing) ,Digital data ,law.invention ,Digital Data Storage ,law ,Computer data storage ,Electronic engineering ,Demodulation ,Microform ,Electrical and Electronic Engineering ,business ,Decoding methods ,Communication channel - Abstract
Photographic microfilm has become a promising medium for long-term storage of digital data. We present an end-to-end channel model of the whole processing chain including a novel soft-output demodulator for channels with non-Gaussian noise, such as film. The proposed channel model describes the digital microfilm storage channel with good preciseness.
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- 2011
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49. Towards rewritable multilevel optical data storage in single nanocrystals
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Nicolas Riesen, Heike Ebendorff-Heidepriem, Yinlan Ruan, Xuanzhao Pan, Tanya M. Monro, Hans Riesen, Jiangbo Zhao, Kate Badek, Riesen, Nicolas, Pan, Xuanzhao, Badek, Kate, Ruan, Yinlan, Monro, Tanya M, Zhao, Jiangbo, Ebendorff-Heidepriem, Heike, and Riesen, Hans
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3D optical data storage ,Photoluminescence ,Materials science ,business.industry ,Doping ,02 engineering and technology ,021001 nanoscience & nanotechnology ,7. Clean energy ,01 natural sciences ,Fluence ,Atomic and Molecular Physics, and Optics ,010309 optics ,Digital Data Storage ,Optics ,Nanocrystal ,0103 physical sciences ,Computer data storage ,Optoelectronics ,0210 nano-technology ,business ,Optical disc - Abstract
Novel approaches for digital data storage are imperative, as storage capacities are drastically being outpaced by the exponential growth in data generation. Optical data storage represents the most promising alternative to traditional magnetic and solid-state data storage. In this paper, a novel and energy efficient approach to optical data storage using rare-earth ion doped inorganic insulators is demonstrated. In particular, the nanocrystalline alkaline earth halide BaFCl:Sm is shown to provide great potential for multilevel optical data storage. Proof-of-concept demonstrations reveal for the first time that these phosphors could be used for rewritable, multilevel optical data storage on the physical dimensions of a single nanocrystal. Multilevel information storage is based on the very efficient and reversible conversion of Sm³⁺ to Sm²⁺ ions upon exposure to UV-C light. The stored information is then read-out using confocal optics by employing the photoluminescence of the Sm²⁺ ions in the nanocrystals, with the signal strength depending on the UV-C fluence used during the write step. The latter serves as the mechanism for multilevel data storage in the individual nanocrystals, as demonstrated in this paper. This data storage platform has the potential to be extended to 2D and 3D memory for storage densities that could potentially approach petabyte/cm³ levels. Refereed/Peer-reviewed
- Published
- 2018
- Full Text
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50. Design of the Tracking Controller for Holographic Digital Data Storage
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Masayoshi Tomizuka, Bong Sik Kwak, Choong Woo Lee, and Chung Choo Chung
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Computer science ,Feed forward ,Servomechanism ,Holographic data storage ,Computer Science Applications ,law.invention ,Tracking error ,Digital Data Storage ,Control and Systems Engineering ,law ,Control theory ,Control system ,Digital control ,Electrical and Electronic Engineering - Abstract
In this paper, we present a new tracking control method for holographic digital data storage systems. Holographic data storage systems that use disk media need a different tracking method from those that use optical and hard disk drives. Here, we present the design and implementation of the controller. Due to the intermittent characteristics of the tracking error signal (TES), the tracking controller is designed to regulate the tracking error only while valid TES is generated. Since the valid TES appears intermittently, we use a feedforward controller while the TES is not valid. Furthermore, the feedback control and the feedforward control are mode-switched depending on the RF sum signal level. We also show the stability of the closed-loop system employing the mode-switching controller. Experimental results show the effectiveness of the proposed tracking control algorithm. For a ±100 ?m repeatable run out at 1 Hz, we were able to reduce the TES to 3.13 ?m (1?) with mode-switching control.
- Published
- 2010
- Full Text
- View/download PDF
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