Storage Codes Research Articles

Storage codes and recoverable systems on lines and grids

Storage codes and recoverable systems on lines and grids

The BCH Family of Storage Codes on Triangle-Free Graphs and Its Relation to R(3,t)

The BCH Family of Storage Codes on Triangle-Free Graphs and Its Relation to R(3,t)

Storage Codes on Coset Graphs with Asymptotically Unit Rate

Storage Codes on Coset Graphs with Asymptotically Unit Rate

Private information retrieval from locally repairable databases with colluding servers

We consider information-theoretical private information retrieval (PIR) from a coded database with colluding servers. We target, for the first time, locally repairable storage codes (LRCs). We consider any number of local groups g, locality r, local distance δ and dimension k. Our main contribution is a PIR scheme for maximally recoverable (MR) LRCs based on linearized Reed–Solomon codes, which achieve the smallest field sizes among MR-LRCs for many parameter regimes. In our scheme, nodes are identified with codeword symbols and servers are identified with local groups of nodes. Only locally non-redundant information is downloaded from each server, that is, only r nodes (out of r+δ−1) are downloaded per server. The PIR scheme achieves the (download) rate R=(N−k−rt+1)/N, where N=gr is the length of the MDS code obtained after removing the local parities, and for any t colluding servers such that k+rt≤N. For an unbounded number of stored files, the obtained rate is strictly larger than those of known PIR schemes that work for any MDS code. Finally, the obtained PIR scheme can also be adapted when communication between the user and each server is performed via linear network coding, achieving the same rate as previous PIR schemes for this scenario but with polynomial finite field sizes, instead of exponential. Our rates are equal to those of PIR schemes for Reed–Solomon codes, but Reed–Solomon codes are incompatible with the MR-LRC property or linear network coding, thus our PIR scheme is less restrictive in its applications.

Expert consensus on the biobank development of oral genetic diseases and rare diseases and storage codes of related biological samples from craniofacial and oral region

The biological samples of oral genetic diseases and rare diseases are extremely precious. Collecting and preserving these biological samples are helpful to elucidate the mechanisms and improve the level of diagnose and treatment of oral genetic diseases and rare diseases. The standardized construction of biobanks for oral genetic diseases and rare diseases is important for achieving these goals. At present, there is very little information on the construction of these biobanks, and the standards or suggestions for the classification and coding of biological samples from oral and maxillofacial sources, and this is not conducive to the standardization and information construction of biobanks for special oral diseases. This consensus summarizes the background, necessity, principles, and key points of constructing the biobank for oral genetic diseases and rare diseases. On the base of the group standard "Classification and Coding for Human Biomaterial" (GB/T 39768-2021) issued by the National Technical Committee for Standardization of Biological Samples, we suggest 76 new coding numbers for different of biological samples from oral and maxillofacial sources. We hope the consensus may promote the standardization, and smartization on the biobank construction as well as the overall research level of oral genetic diseases and rare diseases in China.

Construction of storage codes of rate approaching one on triangle-free graphs

Construction of storage codes of rate approaching one on triangle-free graphs

GCNSA: DNA storage encoding with a graph convolutional network and self-attention

DNA Encoding, as a key step in DNA storage, plays an important role in reading and writing accuracy and the storage error rate. However, currently, the encoding efficiency is not high enough and the encoding speed is not fast enough, which limits the performance of DNA storage systems. In this work, a DNA storage encoding system with a graph convolutional network and self-attention (GCNSA) is proposed. The experimental results show that DNA storage code constructed by GCNSA increases by 14.4% on average under the basic constraints, and by 5%-40% under other constraints. The increase of DNA storage codes effectively improves the storage density of 0.7-2.2% in the DNA storage system. The GCNSA predicted more DNA storage codes in less time while ensuring the quality of codes, which lays a foundation for higher read and write efficiency in DNA storage.

RepairNatrix: a Snakemake workflow for processing DNA sequencing data for DNA storage.

There has been rapid progress in the development of error-correcting and constrained codes for DNA storage systems in recent years. However, improving the steps for processing raw sequencing data for DNA storage has a lot of untapped potential for further progress. In particular, constraints can be used as prior information to improve the processing of DNA sequencing data. Furthermore, a workflow tailored to DNA storage codes enables fair comparisons between different approaches while leading to reproducible results. We present RepairNatrix, a read-processing workflow for DNA storage. RepairNatrix supports preprocessing of raw sequencing data for DNA storage applications and can be used to flag and heuristically repair constraint-violating sequences to further increase the recoverability of encoded data in the presence of errors. Compared to a preprocessing strategy without repair functionality, RepairNatrix reduced the number of raw reads required for the successful, error-free decoding of the input files by a factor of 25-35 across different datasets. RepairNatrix is available on Github: https://github.com/umr-ds/repairnatrix.

Storage Codes With Flexible Number of Nodes

This paper presents flexible storage codes, a class of error-correcting codes that can recover information from a flexible number of storage nodes. As a result, one can make better use of the available storage nodes in the presence of unpredictable node failures and reduce the data access latency. Assume a storage system encodes <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$k\ell $ </tex-math></inline-formula> information symbols over a finite field <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\mathbb {F}$ </tex-math></inline-formula> into <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$n$ </tex-math></inline-formula> nodes, each of size <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\ell $ </tex-math></inline-formula> symbols. The code is parameterized by a set of tuples <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\{(R_{j},\ell _{j}): 1 \le j \le a\}$ </tex-math></inline-formula> , satisfying <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\ell _{1} &lt; \ell _{2} &lt; {\dots } &lt; \ell _{a} = \ell $ </tex-math></inline-formula> and <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$R_{1}&gt;R_{2}&gt; {\dots }&gt;R_{a}$ </tex-math></inline-formula> , such that the information symbols can be reconstructed from any <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$R_{j}$ </tex-math></inline-formula> nodes, each node accessing <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\ell _{j}$ </tex-math></inline-formula> symbols, for any <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$1 \le j \le a$ </tex-math></inline-formula> . In other words, the code allows a flexible number of nodes for decoding to accommodate the variance in the data access time of the nodes. Code constructions are presented for different storage scenarios, including LRC (locally recoverable) codes, PMDS (partial MDS) codes, and MSR (minimum storage regenerating) codes. We analyze the latency of accessing information and perform simulations on Amazon clusters to show the efficiency of the presented codes.

New Storage Codes Between the MSR and MBR Points Through Block Designs

New Storage Codes Between the MSR and MBR Points Through Block Designs

High-Rate Storage Codes on Triangle-Free Graphs

Consider an assignment of bits to the vertices of a connected graph <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$G(V,E)$ </tex-math></inline-formula> with the property that the value of each vertex is a function of the values of its neighbors. A collection of such assignments is called a storage code of length <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$|V|$ </tex-math></inline-formula> on <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$G$ </tex-math></inline-formula> . The storage code problem can be equivalently formulated as maximizing the probability of success in a guessing game on graphs, or constructing index codes of small rate. If <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$G$ </tex-math></inline-formula> contains many cliques, it is easy to construct codes of rate close to 1, so a natural problem is to construct high-rate codes on triangle-free graphs, where constructing codes of rate <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$&gt; 1/2$ </tex-math></inline-formula> is a nontrivial task, with few known results. In this work we construct infinite families of linear storage codes with high rate relying on coset graphs of binary linear codes. We also derive necessary conditions for such codes to have high rate, and even rate potentially close to one. We also address correction of multiple erasures in the codeword, deriving recovery guarantees based on expansion properties of the graph. Finally, we point out connections between linear storage codes and quantum CSS codes, a link to bootstrap percolation and contagion spread in graphs, and formulate a number of open problems.

Levy Equilibrium Optimizer algorithm for the DNA storage code set.

The generation of massive data puts forward higher requirements for storage technology. DNA storage is a new storage technology which uses biological macromolecule DNA as information carrier. Compared with traditional silicon-based storage, DNA storage has the advantages of large capacity, high density, low energy consumption and high durability. DNA coding is to store data information with as few base sequences as possible without errors. Coding is a key technology in DNA storage, and its results directly affect the performance of storage and the integrity of data reading and writing. In this paper, a Levy Equilibrium Optimizer (LEO) algorithm is proposed to construct a DNA storage code set that satisfies combinatorial constraints. The performance of the proposed algorithm is tested on 13 benchmark functions, and 4 new global optima are obtained. Under the same constraints, the DNA storage code set is constructed. Compared with previous work, the lower bound of DNA storage code set is improved by 4-13%.

Robust private information retrieval for low encoding/decoding complexity distributed storage

AbstractPrivate information retrieval (PIR) means a user retrieves a file while revealing no information on which file is being retrieved. In classic PIR, the user needs to wait for the responses of all the storage nodes. However, in general, there may be some nodes that are unresponsive, in which case it is formulated as v‐robust PIR in the network coding (NC) structured distributed storage system (DSS), where v denotes the number of unresponsive nodes. We consider PIR with unresponsive nodes under the framework of NC structured DSS. In particular, the storage nodes adopt combination property with zigzag decodable (CP‐ZD) storage code since it has the advantage of extremely low decoding complexity, which is promised by zigzag decoding (ZD) within a binary field. We design a v‐robust PIR scheme with its download communication cost slightly larger than existing studies, but its decoding complexity is significantly reduced when compared with existing studies.

Adherence to WHO vaccine storage codes and vaccine cold chain management practices at primary healthcare facilities in Dalocha District of Silt'e Zone, Ethiopia

BackgroundThe main elements of effective vaccine cold chain management at the immunization service delivery point are well-trained vaccine cold chain handlers, vaccine storage equipment, and appropriate vaccine management procedures. Vaccine cold chain handlers must have enough expertise to provide the correct vaccine at the right time, maintain vaccine potency, and minimize vaccination failures. The study assessed knowledge of vaccine cold chain handlers on vaccine cold chain management, adherence to the WHO vaccine storage codes and vaccine cold chain management practice at primary health facilities in Dalocha district of Silt'e zone.MethodInstitutional-based cross-sectional study was done at twenty-eight primary health facilities. One hundred forty primary health workers were drawn from four health centers and twenty-four health posts operating in Dalocha woreda of Silt'e zone, SNNPR, Ethiopia. A self-administered questionnaires and on-spot observation checklists were adapted from the WHO and WHO-UNICEF-effective vaccine management assessment tools to collect data from cold chain unit of the primary healthcare facilities. Data were entered to EPI data version 3.1; exported and analyzed using SPSS version 22. Statistical analysis was carried out to determine the level of knowledge, adherence to WHO cold chain management guideline and vaccine handling practice. The relationship that the knowledge of primary healthcare workers, primary healthcare workers training status, primary healthcare facilities' adherence to WHO vaccine storage codes, and length of work experience of primary health care workers have with the vaccine management practice were also exploredResultAbove Half (54%) of the respondents have satisfactory knowledge of vaccine cold chain management. One hundred (71.4%) vaccine cold chain handlers did point correctly to the recommended range of temperature (2°C -8°C) for vaccine storage. Around two-thirds (63.6%) of them were aware of the twice-daily temperature recordings. Nearly half, (46.2%) of primary healthcare facilities have experienced poor adherence to the WHO storage practice codes. Around three-fifths of the observed primary healthcare facilities have registered undesirable vaccine management practices. The primary healthcare workers who received training on vaccine cold chain management (χ2 = 0.058, p=0.015), served at primary health care facilities for more five years (χ2 =18.545, p≤0.001), shown good adherence to WHO vaccine storage code (χ2 =18.545, p≤0.001), have sufficient knowledge on vaccine cold chain management (χ2=4.210, p≤0.031) were all significantly associated with desirable vaccine cold chain management practice.ConclusionThere is a gap in vaccine cold chain handlers’ knowledge about vaccine cold chain management and less than desirable adherence to WHO vaccine storage codes at primary healthcare facilities in Dalocha district. The majority of the observed primary health facilities have registered poor vaccine management practices. Everyone who has a stake in the cold chain management of vaccines should do their share, individually and collectively, to guarantee that everyone reaps the benefits of an effective cold chain.

A subspace regenerating code with minimum decoding bandwidth

Hollmann built a theoretical framework for subspace regenerating storage code. In this framework, a storage node is equipped with a constant dimension subspace chosen from an overall message space F q m ${\bm{F}}_{\bm{q}}^{\bm{m}}$ . The projection of user message on the subspace is stored on the corresponding node. A subspace code needs to fulfil decoding and repairing functionality. The framework stipulates the property for subspace storage code, but a simple implementable construction is still missing. To decrease the complexity of code design as well as encoding and decoding, this article proposed a subspace code implementation over F2 with the parameters of ( m , m , 2 , ⌈ m 2 ⌉ , r , β ) $({\bm{m}},{\bm{m}},2,\lceil {\frac{{\bm{m}}}{2}} \rceil ,{\bm{\ r}},{\bm{\beta }})$ . It is proved theoretically the code is characterized by minimum decoding bandwidth, minimum storage, and exact repair. Still, the code is explicit, feasible and lightweight. A series of examples are given to elucidate the encoding, decoding and repairing procedures, which show in cases of m ≤ 5, the code could achieve high repair efficiency by combining with network coding.

Coding for Scalable Blockchains via Dynamic Distributed Storage

Blockchains store transaction data in the form of a distributed ledger where each node in the network stores a current copy of the sequence of transactions as a hash chain. This requirement of storing the entire ledger incurs a high storage cost that grows undesirably large for high transaction rates and large networks. In this work we use secret key sharing, private key encryption, and distributed storage to design a coding scheme such that each node stores only a part of each transaction, thereby reducing the cold storage cost to a fraction of its original cost. In addition, the storage code ensures the security of the storage from active adversaries that may aim to corrupt prior transactions by altering copies of the ledger. We further employ a dynamic zone allocation algorithm that spreads the node allocation and data distribution across transactions. Under this coding scheme we show that we can also improve the integrity of the transaction data in the network over current schemes.

Combinatorial constraint coding based on the EORS algorithm in DNA storage.

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.

Cold Chain Maintenance and Vaccine Stock Management Practices at Public Health Centers Providing Child Immunization Services in Jimma Zone, Oromia Regional State, Ethiopia: Multi-Centered, Mixed Method Approach.

BackgroundCold chain maintenance is the spine of an immunization program.ObjectiveTo examine the status of cold chain maintenance and evaluate knowledge of cold chain handlers and practices of vaccine management at public health centers providing immunization services in Jimma zone.MethodsAn institutional-based cross-sectional study supplemented with a qualitative method was conducted in 41 randomly selected health centers providing immunization service in districts of Jimma zone from October 31 to November 30, 2019. Pre-tested self-administered questionnaires and observation checklists developed from an effective vaccine management assessment tool (EVMAT) were used to collect quantitative data. Key informants were selected using the purposive sampling technique and an in-depth interview was conducted. Quantifiable data were analyzed using SPSS version 20 and chi-square was used to test the presence of association (p-value <0.05). Qualitative data were analyzed by thematic analysis and triangulated with quantitative findings.ResultsAll public health centers had at least functional ice-lined refrigerators while 28 (68.3%) public health centers had functional deep freezers. Of the cold chain handlers, 120 (82.9%) had fair knowledge. Vaccine storage was appropriate per the World Health Organization's vaccine storage code in ice-lined refrigerators in 11 (24.4%) public health centers. Cold chain handlers’ years of service, types of training, availability of funds for cold chain maintenance, and availability of cold chain equipment at public health centers showed the presence of significant association with vaccine cold chain management practice.ConclusionThe majority of cold chain handlers showed inadequate knowledge while a significant number showed poor practice of preserving the vaccines’ cold chain. Cold chain maintenance was not adequate in public health centers, necessitating attentive efforts of providing proper management of vaccine cold chains at immunization delivery points.

Implementasi Teknologi Blockchain Proof of Work Pada Penelusuran Supply Chain Produk Komputer

In recent times, the supply chain has developed into a large ecosystem. Various products moving from party to party require cooperation between stakeholders in managing the data generated. The problem is that every company has its own transaction records that can be inconsistent and their storage is centralized and not integrated between companies. This makes transaction records easy to falsify. Efficient data management is needed from the producer to the store so that consumers can trust the product. Therefore, the authors designed a product tracking system using blockchain by implementing proof of work (PoW) as the consensus algorithm, SHA-3 256 as data security, Mongo database as cloud-based data storage and QR Code as the output. As a result, transaction data from producers, distributors to retail stores are stored completely in MongoDB which is a cloud-based database, then the resulting QR Code can be used to view details of producers, distributors to retail stores that sell them. The simulation and trial results show the product tracing system design is successful as expected.&#x0D;

Download Time Analysis for Distributed Storage Codes With Locality and Availability

The paper presents techniques for analyzing the expected download time in distributed storage systems that employ systematic availability codes. These codes provide access to hot data through the systematic server containing the object and multiple recovery groups. When a request for an object is received, it can be replicated (forked) to the systematic server and all recovery groups. We first consider the low-traffic regime and present the close-form expression for the download time. By comparison across systems with availability, maximum distance separable (MDS), and replication codes, we demonstrate that availability codes can reduce download time in some settings but are not always optimal. In the high-traffic regime, the system contains multiple inter-dependent Fork-Join queues, making exact analysis intractable. Accordingly, we present upper and lower bounds on the download time, and an M/G/1 queue approximation for several cases of interest. Via extensive numerical simulations, we evaluate our bounds and demonstrate that the M/G/1 queue approximation has a high degree of accuracy.