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Data sizes that cannot be processed by conventional data storage and analysis systems are named as Big Data.It also refers to nex technologies developed to store, process and analyze large amounts of data. Automatic information retrieval…
DNA is not only the genetic material of life, but also a favorable material for a new computing model. Various research works based on DNA computing have been carried out in recent years. DNA sequence design is the foundation of such…
DNA emerges as a promising medium for the exponential growth of digital data due to its density and durability. This study extends recent research by addressing the \emph{coverage depth problem} in practical scenarios, exploring optimal…
Storing big data directly on a blockchain poses a substantial burden due to the need to maintain a consistent ledger across all nodes. Numerous studies in decentralized storage systems have been conducted to tackle this particular…
1. Natural sounds have been recorded for millions of hours over the previous decades using passive acoustic monitoring. Improvements in deep learning models have vastly accelerated the analysis of large portions of this data. While new…
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…
Software has long been established as an essential aspect of the scientific process in mathematics and other disciplines. However, reliably referencing software in scientific publications is still challenging for various reasons. A crucial…
In the near future, all the human genes will be identified. But understanding the functions coded in the genes is a much harder problem. For example, by using block entropy, one has that the DNA code is closer to a random code then written…
Many scientific and practical areas have shown increasing interest in reaping the benefits of blockchain technology to empower software systems. However, the unique characteristics and requirements associated with Blockchain Based Software…
The conjunction of insights from structural biology, solution biochemistry, genetics and single molecule biophysics has provided a renewed impetus for the construction of quantitative models of biological processes. One area that has been a…
This paper presents a memory-optimized metadata-based data structure for implementation of binary chromosome in Genetic Algorithm. In GA different types of genotypes are used depending on the problem domain. Among these, binary genotype is…
DNA Data storage has recently attracted much attention due to its durable preservation and extremely high information density (bits per gram) properties. In this work, we propose a hybrid coding strategy comprising of generalized…
Writing complex computer programs to study scientific problems requires careful planning and an in-depth knowledge of programming languages and tools. In this chapter the importance of using the right tool for the right problem is…
While metagenomics has emerged as a technology of choice for analyzing bacterial populations, assembly of metagenomic data remains difficult thus stifling biological discoveries. metaSPAdes is a new assembler that addresses the challenge of…
Software systems are getting more complex as the system grows where maintaining such system is a primary concern for the industry. Code clone is one of the factors making software maintenance more difficult. It is a process of replicating…
Reservoir computing is a type of a recurrent neural network, mapping the inputs into higher dimensional space using fixed and nonlinear dynamical systems, called reservoirs. In the literature, there are various types of reservoirs ranging…
We describe a grammar for DNA sequencing reads from which we can compute the BWT directly. Our motivation is to perform in succinct space genomic analyses that require complex string queries not yet supported by repetition-based…
With the explosive increase of big data in industry and academic fields, it is necessary to apply large-scale data processing systems to analysis Big Data. Arguably, Spark is state of the art in large-scale data computing systems nowadays,…
With the rapid increase of available digital data, DNA storage is identified as a storage media with high density and capability of long-term preservation, especially for archival storage systems. However, the encoding density (i.e., how…
Computational biology continues to spread into new fields, becoming more accessible to researchers trained in the wet lab who are eager to take advantage of growing datasets, falling costs, and novel assays that present new opportunities…