A Survey of Processing Systems for Phylogenetics and Population Genetics

IF 3.1 4区计算机科学 Q2 COMPUTER SCIENCE, HARDWARE & ARCHITECTURE ACM Transactions on Reconfigurable Technology and Systems Pub Date : 2023-03-16 DOI:10.1145/3588033

Reinout Corts, Nikolaos S. Alachiotis

引用次数: 0

Abstract

The COVID-19 pandemic brought Bioinformatics into the spotlight, revealing that several existing methods, algorithms, and tools were not well prepared to handle large amounts of genomic data efficiently. This led to prohibitively long execution times and the need to reduce the extent of analyses to obtain results in a reasonable amount of time. In this survey, we review available high-performance computing and hardware-accelerated systems based on FPGA and GPU technology. Optimized and hardware-accelerated systems can conduct more thorough analyses considerably faster than pure software implementations, allowing to reach important conclusions in a timely manner to drive scientific discoveries. We discuss the reasons that are currently hindering high-performance solutions from being widely deployed in real-world biological analyses and describe a research direction that can pave the way to enable this.

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系统发育与群体遗传学处理系统综述

2019冠状病毒病大流行使生物信息学成为人们关注的焦点，揭示了一些现有的方法、算法和工具尚未为有效处理大量基因组数据做好充分准备。这导致执行时间过长，并且需要减少分析的范围，以便在合理的时间内获得结果。在本调查中，我们回顾了基于FPGA和GPU技术的现有高性能计算和硬件加速系统。优化和硬件加速的系统可以比纯软件实现更快地进行更彻底的分析，从而及时得出重要的结论，从而推动科学发现。我们讨论了目前阻碍高性能解决方案在现实世界生物分析中广泛应用的原因，并描述了一个可以为实现这一目标铺平道路的研究方向。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

ACM Transactions on Reconfigurable Technology and Systems COMPUTER SCIENCE, HARDWARE & ARCHITECTURE-

CiteScore

4.90

自引率

8.70%

发文量

审稿时长

>12 weeks

期刊介绍： TRETS is the top journal focusing on research in, on, and with reconfigurable systems and on their underlying technology. The scope, rationale, and coverage by other journals are often limited to particular aspects of reconfigurable technology or reconfigurable systems. TRETS is a journal that covers reconfigurability in its own right. Topics that would be appropriate for TRETS would include all levels of reconfigurable system abstractions and all aspects of reconfigurable technology including platforms, programming environments and application successes that support these systems for computing or other applications. -The board and systems architectures of a reconfigurable platform. -Programming environments of reconfigurable systems, especially those designed for use with reconfigurable systems that will lead to increased programmer productivity. -Languages and compilers for reconfigurable systems. -Logic synthesis and related tools, as they relate to reconfigurable systems. -Applications on which success can be demonstrated. The underlying technology from which reconfigurable systems are developed. (Currently this technology is that of FPGAs, but research on the nature and use of follow-on technologies is appropriate for TRETS.) In considering whether a paper is suitable for TRETS, the foremost question should be whether reconfigurability has been essential to success. Topics such as architecture, programming languages, compilers, and environments, logic synthesis, and high performance applications are all suitable if the context is appropriate. For example, an architecture for an embedded application that happens to use FPGAs is not necessarily suitable for TRETS, but an architecture using FPGAs for which the reconfigurability of the FPGAs is an inherent part of the specifications (perhaps due to a need for re-use on multiple applications) would be appropriate for TRETS.