Proceedings of the International MultiConference of Engineers and Computer Scientists, Vol II, IMECS 2009

Recent advances in DNA sequencing technology and their focal role in Genome Wide Association Studies (GWAS) have rekindled a growing interest in the whole-genome sequence assembly (WGSA) problem, thereby, inundating the field with a plethora of new formalizations, algorithms, heuristics and implementations. And yet, scant attention has been paid to comparative assessments of these assemblers' quality and accuracy. No commonly accepted and standardized method for comparison exists yet. Even worse, widely used metrics to compare the assembled sequences emphasize only size, poorly capturing the contig quality and accuracy. This paper addresses these concerns: it highlights common anomalies in assembly accuracy through a rigorous study of several assemblers, compared under both standard metrics (N50, coverage, contig sizes, etc.) as well as a more comprehensive metric (Feature-Response Curves, FRC) that is introduced here; FRC transparently captures the trade-offs between contigs' quality against their sizes. For this purpose, most of the publicly available major sequence assemblers – both for low-coverage long (Sanger) and high-coverage short (Illumina) reads technologies – are compared. These assemblers are applied to microbial (Escherichia coli, Brucella, Wolbachia, Staphylococcus, Helicobacter) and partial human genome sequences (Chr. Y), using sequence reads of various read-lengths, coverages, accuracies, and with and without mate-pairs. It is hoped that, based on these evaluations, computational biologists will identify innovative sequence assembly paradigms, bioinformaticists will determine promising approaches for developing “next-generation” assemblers, and biotechnologists will formulate more meaningful design desiderata for sequencing technology platforms. A new software tool for computing the FRC metric has been developed and is available through the AMOS open-source consortium.

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Comparing de novo genome assembly: the long and short of it.

With the evolution of the fifth-generation (5G) wireless network, the Internet of Things (IoT) has become a revolutionary technique that enables a diverse number of features and applications. It can able a diverse amount of devices to be connected in order to create a single communication architecture. As it has significantly expanded in recent years, it is fundamental to study this trending technology in detail and take a close look at its applications in the different domains. It represents an enabler of new communication possibilities between people and things. The main asset of this concept is its significant influence through the creation of a new world dimension. The key features required for employing a large-scale IoT are low-cost sensors, high-speed and error-tolerant data communications, smart computations, and numerous applications. This research work is presented in four main sections, including a general overview of IoT technology, a summary of previous correlated surveys, a review regarding the main IoT applications, and a section on the challenges of IoT. The purpose of this study is to fully cover the applications of IoT, including healthcare, environmental, commercial, industrial, smart cities, and infrastructural applications. This work explains the concept of IoT and defines and summarizes its main technologies and uses, offering a next-generation protocol as a solution to the challenges. IoT challenges were investigated to enhance research and development in the fields. The contribution and weaknesses of each research work cited are covered, highlighting eventual possible research questions and open matters for IoT applications to ensure a full analysis coverage of the discussed papers.

https://www.mdpi.com/2073-8994/12/10/1674/pdf

Internet of Things and Its Applications: A Comprehensive Survey

The Internet of Things (IoTs) enables coupling of digital and physical objects using worthy communication technologies and introduces a future vision where computing systems, users and objects cooperate for convenience and economic benefits. Such a vision requires seamless security, data privacy, authentication and robustness against attacks. These attributes can be introduced by blockchain, a distributed ledger that maintains an immutable log of network transactions. In this paper, we present a comprehensive review on how to remodel blockchain to the specific IoT needs in order to develop Blockchain based IoT (BIoT) applications and aim to shape a coherent picture of the current state-of-the-art efforts in this direction. After describing the basic characteristics and requirements of IoT, evolution of blockchain is presented. In this regard, we start with the fundamental working principles of blockchain and how such systems achieve auditability, security and decentralization. Further, we describe the most relevant BIoT applications, its architecture design and security aspects. From there, we build our narrative on the centralized IoT challenges followed by recent advances towards solving them. Finally, some future directions are enumerated with the aim to guide future BIoT researchers on challenges that needs to be considered ahead of deploying the next generation of BIoT applications.

Unification of Blockchain and Internet of Things (BIoT): requirements, working model, challenges and future directions

In this paper, we study the embedding of cycles in twisted cubes. It has been proven in the literature that, for any integer l, 4 ≤ l ≤ 2 n , a cycle of length l can be embedded with dilation 1 in an n-dimensional twisted cube, n ≥ 3. We obtain a stronger result of embedding of cycles with edge-pancyclic. We prove that, for any integer l, 4 ≤ l ≤ 2 n , and a given edge (x, y) in an n-dimensional twisted cube, n ≥ 3, a cycle C of length l can be embedded with dilation 1 in the n-dimensional twisted cube such that (x, y) is in C in the twisted cube. Based on the proof of the edge-pancyclicity of twisted cubes, we further provide an O (l log l+ n 2 + nl) algorithm to find a cycle C of length l that contains (u, v) in T Q n for any (u, v) ∈ E(TQ n ) and any integer l with 4 ≤ l ≤ 2 n .

Ruo-Wei Hung

Papers

Linear-time algorithms for the Hamiltonian problems on distance-hereditary graphs

Embedding two edge-disjoint Hamiltonian cycles into locally twisted cubes

Solving the path cover problem on circular-arc graphs by using an approximation algorithm

Linear-time certifying algorithms for the path cover and Hamiltonian cycle problems on interval graphs

Finding a minimum path cover of a distance-hereditary graph in polynomial time