Person: Gupta, Manish K
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Manish K Gupta
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Publication Metadata only On conflict free DNA codes(Springer, 01-01-2021) Benerjee, Krishna Gopal; Deb, Sourav; Gupta, Manish K; Gupta, Manish K; Gupta, Manish K; Gupta, Manish K; Gupta, Manish K; Gupta, Manish K; DA-IICT, Gandhinagar; Benerjee, Krishna Gopal (201221007); Deb, Sourav (201721012)DNA storage has emerged as an important area of research. The reliability of a DNA storage system depends on designing those DNA strings (called DNA codes) that are sufficiently dissimilar. In this work, we introduce DNA codes that satisfy the newly introduced constraint, a generalization of the non-homopolymers constraint. In particular, each codeword of the DNA code has the specific property that any two consecutive sub-strings of the DNA codeword will not be the same. This is apart from the usual constraints such as Hamming, reverse, reverse-complement and�GC-content. We believe that the new constraints proposed in this paper will provide significant achievements in reducing the errors, during reading and writing data into the synthetic DNA strings. We also present a construction (based on a variant of stochastic local search algorithm) to determine the size of the DNA codes with a constraint that each DNA codeword is free from secondary structures in addition to the usual constraint. This further improves the lower bounds from the existing literature, in some specific cases. A recursive isometric map between binary vectors and DNA strings is also proposed. By applying this map over the well known binary codes, we obtain classes of DNA codes with all of the above constraints, including the property that the constructed DNA codewords are free from the hairpin like secondary structures.Publication Metadata only Bounds on generalized FR codes using hypergraphs(Springer, 01-02-2021) Gopal, Krishna; Gupta, Manish K; Gupta, Manish K; Gupta, Manish K; Gupta, Manish K; Gupta, Manish K; Gupta, Manish K; DA-IICT, GandhinagarIn the Distributed Storage Systems (DSSs), the encoded fraction of information is stored in a distributed fashion on different chunk servers. Recently a new paradigm of Fractional Repetition (FR) codes has been introduced, in which, encoded data information is stored on distributed servers using an encoding involving a Maximum Distance Separable (MDS) code and a Repetition code. In this work, we have considered FR codes with asymmetric parameters known as Generalized Fractional Repetition (GFR) codes. We have shown that any GFR code is equivalent to a hypergraph. Using the correspondence, the properties and the bounds of a hypergraph are directly mapped to the associated GFR code. In general, using the correspondence, the necessary and sufficient conditions for the existence of a GFR code is obtained. It is also shown that any GFR code associated with a linear hypergraph is universally good, and any locally repairable GFR code is associated with a class of non-linear hypergraph.Publication Metadata only DNA Code Design Based on the Cosets of Codes over Z4(MDPI, 22-11-2023) Alahmadi, Adel N; Melibari, Fatimah Anas; Gupta, Manish K; Gupta, Manish K; Gupta, Manish K; Gupta, Manish K; Gupta, Manish K; Gupta, Manish K; DA-IICT, GandhinagarDNA code design is a challenging problem, and it has received great attention in the literature due to its applications in DNA data storage, DNA origami, and DNA computing. The primary focus of this paper is in constructing new DNA codes using the cosets of linear codes over the ring�?4. The Hamming distance constraint, GC-content constraint, and homopolymers constraint are all considered. In this study, we consider the cosets of Simplex alpha code, Kerdock code, Preparata code, and Hadamard code. New DNA codes of lengths four, eight, sixteen, and thirty-two are constructed using a combination of an algebraic coding approach and a variable neighborhood search approach. In addition, good lower bounds for DNA codes that satisfy important constraints have been successfully established using Magma software V2.24-4 and Python 3.10 programming in our comprehensive methodology.Publication Metadata only The yin-yang codec for archival DNA storage(Nature, 25-04-2022) Gupta, Manish K; Gupta, Manish K; Gupta, Manish K; Gupta, Manish K; Gupta, Manish K; Gupta, Manish K; DA-IICT, GandhinagarA robust and reliable codec is the backbone for any digital DNA storage. A recent work introduces a codec based on ancient Chinese philosophy, yin�yang, that outperforms other codecs in terms of reliability and physical information density.Publication Metadata only On non-uniform flower codes(Springer, 01-05-2020) Benerjee, Krishna Gopal; Gupta, Manish K; Gupta, Manish K; Gupta, Manish K; Gupta, Manish K; Gupta, Manish K; Gupta, Manish K; DA-IICT, Gandhinagar; Benerjee, Krishna Gopal (201221007)For a Distributed Storage System (DSS), the�Fractional Repetition�(FR) code is a class in which replicas of encoded data packets are stored on distributed chunk servers, where the encoding is done using the Maximum Distance Separable (MDS) code. The FR codes allow for the exact uncoded repair with minimum repair bandwidth. In this paper, FR codes (called Flower codes) are constructed using finite binary sequences. It is shown that, for any FR code, there exists a Flower code and therefore Flower code is the general framework to construct FR code with uniform as well as non-uniform parameters. The condition for universally good Flower code is calculated on such sequences. For some sequences, the universally good Flower codes and Locally Repairable Flower codes are explored. In addition, conditions for equivalent Flower codes and dual Flower codes are also investigated in this paper. Some families of Flower codes with non-uniform parameters are obtained such that, from those families, Flowers code with uniform parameters are optimal FR codes in the literature. It is shown that any FR code is a Flower code and some known FR codes are obtained as the special cases of Flower codes using sequences.Publication Metadata only Trade-off for Heterogeneous Distributed Storage Systems between Storage and Repair Cost(Springer, 03-04-2021) Benerjee, Krishna Gopal; Gupta, Manish K; Gupta, Manish K; Gupta, Manish K; Gupta, Manish K; Gupta, Manish K; Gupta, Manish K; DA-IICT, Gandhinagar; Benerjee, Krishna Gopal (201221007)We consider heterogeneous distributed storage systems (DSSs) having flexible reconstruction degree, where each node in the system has nonuniform repair bandwidth and nonuniform storage capacity. In particular, a data collector can reconstruct the file using some��nodes in the system and, for a node failure, the system can be repaired by some set of active nodes. Using min-cut bound, we investigate the fundamental trade-off between storage and repair costs for our model of the heterogeneous DSS. Further, the problem is formulated as bi-objective optimization linear programing problem for various heterogeneous DSSs. For some DSSs, it is shown that the calculated min-cut bound is tight.Publication Metadata only On the Classification of Codes over Non-Unital Ring of Order 4(World Scientific Publishing, 27-08-2023) Deb, Sourav; Kikani, Isha; Gupta, Manish K; Gupta, Manish K; Gupta, Manish K; Gupta, Manish K; Gupta, Manish K; Gupta, Manish K; DA-IICT, Gandhinagar; Deb, Sourav (201721012); Kikani, Isha (201901039)In the last 60 years coding theory has been studied a lot over finite fields�Fq�or commutative rings�R�with unity. Although in�1993, a study on the classification of the rings (not necessarily commutative or ring with unity) of order�p2�had been presented, the construction of codes over non-commutative rings or non-commutative non-unital rings surfaced merely two years ago. In this letter, we extend the diverse research on exploring the codes over the non-commutative and non-unital ring�E=?2a=2b=0,a2=a,b2=b,ab=a,ba=b?�by presenting the classification of optimal and nice codes of length�n?7�over�E, along with respective weight enumerators and complete weight enumerators.Publication Metadata only 10 Years of Natural Data Storage(IEEE, 01-12-2022) Limbachiya, Dixita; Gupta, Manish K; Aggarwal, Vaneet; Gupta, Manish K; Gupta, Manish K; Gupta, Manish K; Gupta, Manish K; Gupta, Manish K; DA-IICT, Gandhinagar; Limbachiya, Dixita (201221014)Digital data explosion has been driving a demand for robust and reliable data storage medium. The present day digital storage devices presents a big challenge for data scientists to provide reliable, affordable and dense storage medium. In the last decade, natural storage medium such as DNA, bacteria, and protein has been shown as a promising approach for next generation information storage systems. This article is a review that discusses advancements in the natural data storage, which has potential to replace the current physical storage for archival systems and have high storage per unit weight of medium, and is affordable and reliable. Further, the challenges for natural data storage will also be presented. With the international DNA data storage alliance of more than 30 companies and academic alliance in 2020, one would hope that DNA data storage will soon be available commercially in next 5�10 years. The success of the alliance will also motivate researchers to explore the other natural storage medium such as bacteria and protein which are currently in the lab.Publication Metadata only On the covering radius of some modular codes(AIMS, 01-08-2014) Gupta, Manish K; Durairajan, Chinnappillai; Gupta, Manish K; Gupta, Manish K; Gupta, Manish K; Gupta, Manish K; Gupta, Manish K; DA-IICT, GandhinagarThis paper gives lower and upper bounds on the covering radius of codes over�Z2s�with respect to homogenous distance. We also determine the covering radius of various Repetition codes, Simplex codes (Type�?�and Type�?) and their dual and give bounds on the covering radii for MacDonald codes of both types over�Z4.Publication Metadata only Family of Constrained Codes for Archival DNA Data Storage(IEEE, 01-10-2018) Limbachiya, Dixita; Gupta, Manish K; Aggarwal, Vaneet; Gupta, Manish K; Gupta, Manish K; Gupta, Manish K; Gupta, Manish K; Gupta, Manish K; DA-IICT, Gandhinagar; Limbachiya, Dixita (201221014)DNA-based data storage systems have evolved as a solution to accommodate data explosion. In this letter, some properties of DNA codewords that are essential for an archival DNA storage are considered for the design of codes. Constraint-based DNA codes, which avoid runs of nucleotides, have fixed GC-weight, and a specific minimum distance is presented. An altruistic algorithm that enumerates DNA codewords with the above constraints is provided. A theoretical bound on such DNA codewords is obtained. This bound is tight when there is no minimum distance constraint.