As a first demonstrator of the EDRA approach, we developed a DAE hardware accelerator for a computationally intensive task from the bioinformatics domain, namely the RAxML Phylogenetic Analysis application*.
As shown in the figure above, RAxML’s most computationally intensive task (blue square) is offloaded to the hardware accelerator (step 1); the host CPU sends all input data to the FPGA (step 2), and as soon as processing is done, it receives back the results (step 3). Please note that you need to have an AWS account in order to try the EDRA demo.
*A. Stamatakis: “RAxML Version 8: A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies”. In Bioinformatics, 2014
Recently published articles on research conducted with the RAxML tool
- Nikolaos Alachiotis, Panagiotis Skrimponis, Manolis Pissadakis, Sundeep Rangan, Dionisios Pnevmatikatos, “Near-memory Acceleration for Scalable Phylogenetic Inference”, The 2020 ACM/SIGDA International Symposium on Field-Programmable Gate Arrays
- Maria Vasilarou, Nikolaos Alachiotis, Joanna Garefalaki, Apostolos Beloukas, Pavlos Pavlidis, “Population genomics insights into the recent evolution of SARS-CoV-2”, bioRxiv, 1/1/2020
- Nikolaos Alachiotis, Charalampos Vatsolakis, Grigorios Chrysos, Dionisios Pnevmatikatos, “RAiSD-X: A Fast and Accurate FPGA System for the Detection of Positive Selection in Thousands of Genomes”, ACM Transactions on Reconfigurable Technology and Systems (TRETS), 2019
- Bastian Pfeifer, Nikolaos Alachiotis, Pavlos Pavlidis, Michael G Schimek, “Genome Scans for Selection and Introgression based on k-nearest Neighbor Techniques”, bioRxiv, 1/1/2019
- Nikolaos Alachiotis, Charalampos Vatsolakis, Grigorios Chrysos, Dionisios Pnevmatikatos, “Accelerated Inference of Positive Selection on Whole Genomes”, Field Programmable Logic and Applications, 2018. FPL 2018. International Conference on, 2019
- Nikolaos Alachiotis, Dimitris Theodoropoulos, Dionisios Pnevmatikatos, “Versatile deployment of FPGA accelerators in disaggregated data centers: A bioinformatics case study”, 2017 27th International Conference on Field Programmable Logic and Applications (FPL), 2017
- Pavlos Pavlidis, Daniel Živković, Alexandros Stamatakis, Nikolaos Alachiotis, “SweeD: Likelihood-based detection of selective sweeps in thousands of genomes”, Molecular Biology and Evolution, 2013