High-performance biocomputing for simulating the spread of contagion over large contact networks

Authors:
Keith R. Bisset;Ashwin M. Aji;Madhav V. Marathe;Wu-chun Feng
Affiliations:
Virginia Bioinformatics Inst., Virginia Tech, Blacksburg, USA;Dept. of Computer Science, Virginia Tech, Blacksburg, USA;Virginia Bioinformatics Inst., Dept. of Computer Science, Virginia Tech, Blacksburg, USA;Dept. of Computer Science, Dept. of Elec. & Comp. Eng., Virginia Tech, Blacksburg, USA
Venue:
ICCABS '11 Proceedings of the 2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences
Year:
2011

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Abstract

Many important biological problems can be modeled as contagion diffusion processes over interaction networks. This paper shows how the EpiSimdemics interaction-based simulation system can be applied to the general contagion diffusion problem. Two specific problems, computational epidemiology and human immune system modeling, are given as examples. We then show how the graphics processing unit (GPU) within each compute node of a cluster can effectively be used to speedup the execution of these types of problems by an additional 3.3-fold over a CPU-only solution.