Issue No. 10 - Oct. (2017 vol. 66)
Xian Li , Washington State University, Pullman, WA
Karthi Duraisamy , Washington State University, Pullman, WA
Joe Baylon , Washington State University, Pullman, WA
Turbo Majumder , Intel Labs, Hillsboro, OR
Guopeng Wei , YHGenomics, Chengdu, China
Paul Bogdan , University of Southern California, Los Angeles, CA
Deukhyoun Heo , Washington State University, Pullman, WA
Partha Pratim Pande , Washington State University, Pullman, WA
Understanding the role of competition and cooperation among multiple interacting species of microorganisms that constitute the microbiome and decipher how they enforce homeostasis or trigger diseases requires the development of multi-scale computational models capable of capturing both intra-cell processing (i.e., gene-to-protein interactions) and inter-cell interactions. The multi-scale interdependency that governs the interactions from genes to proteins within a cell and from molecular messengers to cells to microbial communities within the environment raises numerous computation and communication challenges. Internal cell processing cannot be simulated without knowledge of the surroundings. Similarly, cell-cell communication cannot be fully abstracted without stated of internal processing and diffusion effects of molecular messengers. To address the compute- and communication-intensive nature of modeling microbial communities, in this paper, we propose a novel reconfigurable NoC-based manycore architecture capable of simulating a large scale microbial community. The reconfiguration of the NoC topology is achieved through the fractal analysis of NoC traffic and use of the on-chip wireless interfaces. More precisely, we analyze the computational and communication workloads and exploit the observed fractal characteristics for proposing a mathematical strategy for NoC reconfiguration. Experimental results demonstrate that the proposed NoC architecture achieves 56.6 and 62.8 percent improvement in energy delay product over the conventional wireline mesh and flatten butterfly-based high radix NoC architectures, respectively.
Computational modeling, Computer architecture, Wireless communication, Microorganisms, System-on-chip, Microprocessors, Biological system modeling
X. Li et al., "A Reconfigurable Wireless NoC for Large Scale Microbiome Community Analysis," in IEEE Transactions on Computers, vol. 66, no. 10, pp. 1653-1666, 2017.