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Optimizing Reconfigurable Hardware for Genomic Sequences Comparison 优化可重构硬件基因组序列比较
2008 4th Southern Conference on Programmable Logic Pub Date : 2008-03-26 DOI: 10.1109/SPL.2008.4547763
J.J. Marfil, D. Mozos
{"title":"Optimizing Reconfigurable Hardware for Genomic Sequences Comparison","authors":"J.J. Marfil, D. Mozos","doi":"10.1109/SPL.2008.4547763","DOIUrl":"https://doi.org/10.1109/SPL.2008.4547763","url":null,"abstract":"Last advances in the bioinformatics field have lead to improve models and computational resources to satisfy the high computational cost needed to search and identify DNA sequences. This paper provides a FPGA-based systolic array implementation of the Smith-Waterman algorithm, which improves previous proposals, reducing the amount of hardware and the computing power needed. Besides, optimizations in memory access using prefetching and different sizes of the systolic array let us to increase the system's performance up to 60%.","PeriodicalId":372678,"journal":{"name":"2008 4th Southern Conference on Programmable Logic","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2008-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122362714","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
FPGA-Based Acceleration of the Computations Involved in Transcranial Magnetic Stimulation 基于fpga的经颅磁刺激计算加速
2008 4th Southern Conference on Programmable Logic Pub Date : 2008-03-26 DOI: 10.1109/SPL.2008.4547730
O. Creţ, I. Trestian, R. Tudoran, Laura Cret, Lucia Vaicariu
{"title":"FPGA-Based Acceleration of the Computations Involved in Transcranial Magnetic Stimulation","authors":"O. Creţ, I. Trestian, R. Tudoran, Laura Cret, Lucia Vaicariu","doi":"10.1109/SPL.2008.4547730","DOIUrl":"https://doi.org/10.1109/SPL.2008.4547730","url":null,"abstract":"In the last years the interest for magnetic stimulation of the human nervous tissue has increased, because this technique has proved its utility and applicability both as a diagnostic and as a treatment instrument. Research in this domain is aimed at eliminating some disadvantages of the technique: the lack of focalization of the stimulated human body region and the reduced efficiency of the energetic transfer from the stimulating coil to the tissue. Designing better stimulation coils is so far a trial-and-error process, relying on very compute-intensive simulations. In software, such a simulation has a very high running time (several hours for complicated geometries of the coils). This paper proposes and demonstrates an FPGA-based hardware implementation of this simulation, which reduces the computation time by 2-3 orders of magnitude. Thanks to this powerful tool, some significant improvements in the design of the coils have already been obtained.","PeriodicalId":372678,"journal":{"name":"2008 4th Southern Conference on Programmable Logic","volume":"13 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2008-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123479837","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
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