Emulation of biological networks in reconfigurable hardware

Authors:
Natasa Miskov-Zivanov;Andrew Bresticker;Deepa Krishnaswamy;Sreesan Venkatakrishnan;Diana Marculescu;James R. Faeder
Affiliations:
University of Pittsburgh;Carnegie Mellon University;Carnegie Mellon University;Carnegie Mellon University;Carnegie Mellon University;University of Pittsburgh
Venue:
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
Year:
2011

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Abstract

Models of biological networks have been studied through simulations using a number of software tools. However, the intrinsic disparity between the sequential nature of microprocessor architecture used in software-based simulations and the highly parallel nature of biological systems may result in prohibitively long simulation times. In this work, we adopt an alternative approach to simulation of biological systems using hardware-based emulation. Our results on Boolean network models show that such an approach can provide speedup of 17,000X when compared to existing software simulation approaches.