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SUMMARY:FPGA Acceleration of GWAS Permutation Testing
DTSTART;VALUE=DATE-TIME:20211203T104500Z
DTEND;VALUE=DATE-TIME:20211203T111500Z
DTSTAMP;VALUE=DATE-TIME:20260516T045158Z
UID:indico-contribution-1529@events.chpc.ac.za
DESCRIPTION:Speakers: Yaniv Swiel (Wits)\nThe large sample sizes of modern
  genetic datasets has necessitated the development of high-throughput acce
 lerators in order to allow bioinformatics research to be performed in a re
 asonable amount of time. Although the inherently parallel nature of FPGAs 
 makes them well suited to accelerating high-throughput workloads\, they ar
 e not commonly employed as bioinformatics accelerators (in lieu of CPUs an
 d/or GPUs) due to their high cost and the fact that developing FPGA-accele
 rated algorithms is a more complex and time-consuming process than the dev
 elopment of software for CPUs or GPUs. The availability of cloud-based FPG
 A instances\, however\, has made powerful FPGAs accessible to bioinformati
 cs labs and the continuous improvement of FPGA design tools has reduced mu
 ch of the complexity of FPGA development.\n\nThis work determines the effi
 cacy of FPGAs when applied to the acceleration of GWAS permutation testing
  - a computationally expensive bioinformatics algorithm that involves the 
 repeated multiplication of a constant matrix with a changing vector - by p
 resenting the design and evaluation of an FPGA-based accelerator designed 
 to run on an AWS EC2 FPGA instance. \n\nThis work shows that the FPGA acce
 lerator is orders of magnitude faster than a popular CPU-based GWAS tool w
 ithout an apparent loss of accuracy. Furthermore\, this work demonstrates 
 that FPGA acceleration enables the handling of workloads which are almost 
 unfeasible for current CPU-based methods. This work\, therefore\, proves t
 hat FPGAs can effectively accelerate high-throughput bioinformatics worklo
 ads at relatively low cost.\n\nhttps://events.chpc.ac.za/event/98/contribu
 tions/1529/
LOCATION:
URL:https://events.chpc.ac.za/event/98/contributions/1529/
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