Scheduling Large-Scale DNA Sequencing Applications

Scheduling Large-Scale DNA Sequencing Applications

Sudha Gunturu (Oklahoma State University, USA), Xiaolin Li (Oklahoma State University, USA) and Laurence Tianruo Yang (St. Francis Xavier University, Canada)
Copyright: © 2010 |Pages: 17
DOI: 10.4018/978-1-60566-661-7.ch036
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This chapter studies a load scheduling strategy with near-optimal processing time that is designed to explore the computational characteristics of DNA sequence alignment algorithms, specifically, the Needleman-Wunsch Algorithm. Following the divisible load scheduling theory, an efficient load scheduling strategy is designed in large-scale networks so that the overall processing time of the sequencing tasks is minimized. In this study, the load distribution depends on the length of the sequence and number of processors in the network and, the total processing time is also affected by communication link speed. Several cases have been considered in the study by varying the sequences, communication and computation speeds, and number of processors. Through simulation and numerical analysis, this study demonstrates that for a constant sequence length as the numbers of processors increase in the network the processing time for the job decreases and minimum overall processing time is achieved.
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The merging of the two rapid advancing technologies of molecular biology and computer science resulted in a new informatics science, namely bio informatics (Wong Han Min., & Bharadwaj Veeravalli, 2005). Over the past few years, the interest and research in the area of biotechnology has increased drastically. This area of study deals primarily with the methodologies of operating on molecular biological information. The present days of molecular biology is characterized by collection of large volumes of data.

Key Terms in this Chapter

Router: Router is a networking device whose software and hardware are usually tailored to the tasks of routing and forwarding information.

Network Security: Network security consists of the provisions made in an underlying computer network infrastructure, policies adopted by the network administrator to protect the network and the network-accessible resources from unauthorized access and consistent and continuous monitoring and measurement of its effectiveness (or lack) combined together.

Intrusion Detection: Intrusion detection is the act of detecting actions that attempt to compromise the confidentiality, integrity or availability of a resource.

Deep Packet Inspection: Deep Packet Inspection (DPI) is a form of computer network packet filtering that examines the data and/or header part of a packet as it passes an inspection point, searching for protocol non-compliance, viruses, spam, intrusions or predefined criteria to decide if the packet can pass or if it needs to be routed to a different destination, or for the purpose of collecting statistical information. This is in contrast to shallow packet inspection which just checks the header portion of a packet.

Parallel Algorithms: Parallel algorithms are algorithms that can be executed a piece at a time on many different processing devices, and then put back together again at the end to get the correct result.

High-Performance Security Systems: High-performance security systems refer to the software or hardware systems that perform security functions at high performance in terms of processing speed, data, or throughput.

Multi-Core: Multi-core represents a major evolution in the development of processor. A multi-core processor (or chip-level multiprocessor, CMP) combines two or more independent cores (normally a CPU) into a single package composed of a single integrated circuit (IC), called a die, or more dies packaged together.

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