34,359 research outputs found

    Applications and Challenges of Real-time Mobile DNA Analysis

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    The DNA sequencing is the process of identifying the exact order of nucleotides within a given DNA molecule. The new portable and relatively inexpensive DNA sequencers, such as Oxford Nanopore MinION, have the potential to move DNA sequencing outside of laboratory, leading to faster and more accessible DNA-based diagnostics. However, portable DNA sequencing and analysis are challenging for mobile systems, owing to high data throughputs and computationally intensive processing performed in environments with unreliable connectivity and power. In this paper, we provide an analysis of the challenges that mobile systems and mobile computing must address to maximize the potential of portable DNA sequencing, and in situ DNA analysis. We explain the DNA sequencing process and highlight the main differences between traditional and portable DNA sequencing in the context of the actual and envisioned applications. We look at the identified challenges from the perspective of both algorithms and systems design, showing the need for careful co-design

    Nanopore Sequencing Technology and Tools for Genome Assembly: Computational Analysis of the Current State, Bottlenecks and Future Directions

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    Nanopore sequencing technology has the potential to render other sequencing technologies obsolete with its ability to generate long reads and provide portability. However, high error rates of the technology pose a challenge while generating accurate genome assemblies. The tools used for nanopore sequence analysis are of critical importance as they should overcome the high error rates of the technology. Our goal in this work is to comprehensively analyze current publicly available tools for nanopore sequence analysis to understand their advantages, disadvantages, and performance bottlenecks. It is important to understand where the current tools do not perform well to develop better tools. To this end, we 1) analyze the multiple steps and the associated tools in the genome assembly pipeline using nanopore sequence data, and 2) provide guidelines for determining the appropriate tools for each step. We analyze various combinations of different tools and expose the tradeoffs between accuracy, performance, memory usage and scalability. We conclude that our observations can guide researchers and practitioners in making conscious and effective choices for each step of the genome assembly pipeline using nanopore sequence data. Also, with the help of bottlenecks we have found, developers can improve the current tools or build new ones that are both accurate and fast, in order to overcome the high error rates of the nanopore sequencing technology.Comment: To appear in Briefings in Bioinformatics (BIB), 201

    An Approximately Optimal Algorithm for Scheduling Phasor Data Transmissions in Smart Grid Networks

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    In this paper, we devise a scheduling algorithm for ordering transmission of synchrophasor data from the substation to the control center in as short a time frame as possible, within the realtime hierarchical communications infrastructure in the electric grid. The problem is cast in the framework of the classic job scheduling with precedence constraints. The optimization setup comprises the number of phasor measurement units (PMUs) to be installed on the grid, a weight associated with each PMU, processing time at the control center for the PMUs, and precedence constraints between the PMUs. The solution to the PMU placement problem yields the optimum number of PMUs to be installed on the grid, while the processing times are picked uniformly at random from a predefined set. The weight associated with each PMU and the precedence constraints are both assumed known. The scheduling problem is provably NP-hard, so we resort to approximation algorithms which provide solutions that are suboptimal yet possessing polynomial time complexity. A lower bound on the optimal schedule is derived using branch and bound techniques, and its performance evaluated using standard IEEE test bus systems. The scheduling policy is power grid-centric, since it takes into account the electrical properties of the network under consideration.Comment: 8 pages, published in IEEE Transactions on Smart Grid, October 201

    A Case Study in Coordination Programming: Performance Evaluation of S-Net vs Intel's Concurrent Collections

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    We present a programming methodology and runtime performance case study comparing the declarative data flow coordination language S-Net with Intel's Concurrent Collections (CnC). As a coordination language S-Net achieves a near-complete separation of concerns between sequential software components implemented in a separate algorithmic language and their parallel orchestration in an asynchronous data flow streaming network. We investigate the merits of S-Net and CnC with the help of a relevant and non-trivial linear algebra problem: tiled Cholesky decomposition. We describe two alternative S-Net implementations of tiled Cholesky factorization and compare them with two CnC implementations, one with explicit performance tuning and one without, that have previously been used to illustrate Intel CnC. Our experiments on a 48-core machine demonstrate that S-Net manages to outperform CnC on this problem.Comment: 9 pages, 8 figures, 1 table, accepted for PLC 2014 worksho
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