{"title":"系统发育与群体遗传学处理系统综述","authors":"Reinout Corts, Nikolaos Alachiotis","doi":"https://dl.acm.org/doi/10.1145/3588033","DOIUrl":null,"url":null,"abstract":"<p>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.</p>","PeriodicalId":49248,"journal":{"name":"ACM Transactions on Reconfigurable Technology and Systems","volume":"113 ","pages":""},"PeriodicalIF":3.1000,"publicationDate":"2023-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"A Survey of Processing Systems for Phylogenetics and Population Genetics\",\"authors\":\"Reinout Corts, Nikolaos Alachiotis\",\"doi\":\"https://dl.acm.org/doi/10.1145/3588033\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p>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.</p>\",\"PeriodicalId\":49248,\"journal\":{\"name\":\"ACM Transactions on Reconfigurable Technology and Systems\",\"volume\":\"113 \",\"pages\":\"\"},\"PeriodicalIF\":3.1000,\"publicationDate\":\"2023-06-20\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"ACM Transactions on Reconfigurable Technology and Systems\",\"FirstCategoryId\":\"94\",\"ListUrlMain\":\"https://doi.org/https://dl.acm.org/doi/10.1145/3588033\",\"RegionNum\":4,\"RegionCategory\":\"计算机科学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"COMPUTER SCIENCE, HARDWARE & ARCHITECTURE\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"ACM Transactions on Reconfigurable Technology and Systems","FirstCategoryId":"94","ListUrlMain":"https://doi.org/https://dl.acm.org/doi/10.1145/3588033","RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"COMPUTER SCIENCE, HARDWARE & ARCHITECTURE","Score":null,"Total":0}
A Survey of Processing Systems for Phylogenetics and Population Genetics
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.
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.
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