Disease Diagnosis-on-a-chip: Large Scale Networks-on-chip Based Multicore Platform for Protein Folding Analysis

Protein folding is critical for many biological processes. In this work, we propose an NoC-based multi-core platform for protein folding computation. We first identify the speedup bottleneck for applying conventional genetic algorithm on a mesh-based multi-core platform. Then, we address this computation-and communication-intensive problem while taking into account both hardware and software aspects. Specifically, we group the processing cores into islands and propose an NoC-based multicore architecture for intra-and inter-island communication. The high scalability of the proposed platform allows us to integrate from 100 to 1200 cores for the folding computation. We then propose a genetic migration algorithm to take advantage of the massive parallel platform. Our simulation results show that the proposed platform offers near-linear speedup as the number of cores increases. We also report the hardware cost in area and power based on a 100-core FPGA prototype. Copyright 2014 ACM.