Related papers: Coding over Sets for DNA Storage
Modern biological science produces vast amounts of genomic sequence data. This is fuelling the need for efficient algorithms for sequence compression and analysis. Data compression and the associated techniques coming from information…
Regenerating codes provide an efficient way to recover data at failed nodes in distributed storage systems. It has been shown that regenerating codes can be designed to minimize the per-node storage (called MSR) or minimize the…
Erasure coding techniques are getting integrated in networked distributed storage systems as a way to provide fault-tolerance at the cost of less storage overhead than traditional replication. Redundancy is maintained over time through…
In this paper, we present an optical computing method for string data alignment applicable to genome information analysis. By applying moire technique to spatial encoding patterns of deoxyribonucleic acid (DNA) sequences, association…
We investigate the problem of maintaining an encoded distributed storage system when some nodes contain adversarial errors. Using the error-correction capabilities that are built into the existing redundancy of the system, we propose a…
Most DNA sequencing technologies are based on the shotgun paradigm: many short reads are obtained from random unknown locations in the DNA sequence. A fundamental question, studied in arXiv:1203.6233, is what read length and coverage depth…
Constrained sequence codes have been widely used in modern communication and data storage systems. Sequences encoded with constrained sequence codes satisfy constraints imposed by the physical channel, hence enabling efficient and reliable…
DNA has many valuable characteristics that make it suitable for a long-term storage medium, in particular its durability and high information density. DNA can be stored safely for hundreds of years with virtually no degradation, in contrast…
Large-scale distributed storage systems typically use erasure codes to provide durability of data in the face of failures. A set of $k$ blocks to be stored is encoded using an $[n, k]$ code to generate $n$ blocks that are then stored on…
Network codes designed specifically for distributed storage systems have the potential to provide dramatically higher storage efficiency for the same availability. One main challenge in the design of such codes is the exact repair problem:…
A simple DNA-based data storage scheme is demonstrated in which information is written using "addressing" oligonucleotides. In contrast to other methods that allow arbitrary code to be stored, the resulting DNA is suitable for downstream…
Distributed storage systems often introduce redundancy to increase reliability. When coding is used, the repair problem arises: if a node storing encoded information fails, in order to maintain the same level of reliability we need to…
The biochemical processes underlying DNA data storage, including synthesis, amplification, and sequencing, are inherently noisy. Consequently, base-level insertion, deletion, and substitution (IDS) errors, as well as sequence-level…
Motivated by applications in DNA storage, we study a setting in which strings are affected by tandem-duplication errors. In particular, we look at two settings: disjoint tandem-duplication errors, and equal-length tandem-duplication errors.…
To equip DNA-based data storage with random-access capabilities, Yazdi et al. (2018) prepended DNA strands with specially chosen address sequences called primers and provided certain design criteria for these primers. We provide explicit…
Due to its longevity and enormous information density, DNA is an attractive medium for archival storage. In this work, we study the fundamental limits and trade-offs of DNA-based storage systems by introducing a new channel model, which we…
We introduce the sum channel, a new channel model motivated by applications in distributed storage and DNA data storage. In the error-free case, it takes as input an $\ell$-row binary matrix and outputs an $(\ell+1)$-row matrix whose first…
This paper studies two problems that are motivated by the novel recent approach of composite DNA that takes advantage of the DNA synthesis property which generates a huge number of copies for every synthesized strand. Under this paradigm,…
Due to its longevity and enormous information density, DNA is an attractive medium for archival data storage. Thanks to rapid technological advances, DNA storage is becoming practically feasible, as demonstrated by a number of experimental…
This paper presents a novel coding scheme for distributed storage systems containing nodes with adversarial errors. The key challenge in such systems is the propagation of erroneous data from a single corrupted node to the rest of the…