Multiscale Hy3S: hybrid stochastic simulation for supercomputers

BMC Bioinformatics
Howard SalisYiannis N Kaznessis

Abstract

Stochastic simulation has become a useful tool to both study natural biological systems and design new synthetic ones. By capturing the intrinsic molecular fluctuations of "small" systems, these simulations produce a more accurate picture of single cell dynamics, including interesting phenomena missed by deterministic methods, such as noise-induced oscillations and transitions between stable states. However, the computational cost of the original stochastic simulation algorithm can be high, motivating the use of hybrid stochastic methods. Hybrid stochastic methods partition the system into multiple subsets and describe each subset as a different representation, such as a jump Markov, Poisson, continuous Markov, or deterministic process. By applying valid approximations and self-consistently merging disparate descriptions, a method can be considerably faster, while retaining accuracy. In this paper, we describe Hy3S, a collection of multiscale simulation programs. Building on our previous work on developing novel hybrid stochastic algorithms, we have created the Hy3S software package to enable scientists and engineers to both study and design extremely large well-mixed biological systems with many thousands of reactions and chem...Continue Reading

References

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Citations

Aug 9, 2011·ACS Chemical Biology·Katherine VolzingYiannis N Kaznessis
Dec 3, 2008·IET Systems Biology·I I MoraruL M Loew
Aug 14, 2013·Proceedings of the National Academy of Sciences of the United States of America·Patrick Smadbeck, Yiannis N Kaznessis
Jan 20, 2009·Briefings in Bioinformatics·Jürgen Pahle
Oct 13, 2006·Bioinformatics·Stefan HoopsUrsula Kummer
Oct 16, 2007·Bioinformatics·T FournierN Mermod
Sep 2, 2008·Bioinformatics·Anthony D HillYiannis N Kaznessis
Nov 8, 2007·BMC Systems Biology·Yiannis N Kaznessis
Apr 6, 2007·BMC Systems Biology·Vassilios Sotiropoulos, Yiannis N Kaznessis
Sep 9, 2009·BMC Systems Biology·Alina CruduOvidiu Radulescu
Jan 21, 2011·BMC Systems Biology·Konstantinos BiliourisYiannis N Kaznessis
Apr 5, 2014·PLoS Computational Biology·Justin S HoggJames R Faeder
Jul 23, 2014·BioMed Research International·Marco AldinucciAngelo Troina
Jun 20, 2013·Briefings in Bioinformatics·Marco AldinucciMario Coppo
Mar 19, 2009·IET Systems Biology·E E May, R L Schiek
Apr 6, 2011·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Jianyong SunCharlie Hodgman
Aug 1, 2009·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Vassilios SotiropoulosYiannis N Kaznessis
Aug 25, 2015·The Journal of Chemical Physics·Kevin R Sanft, Hans G Othmer
May 17, 2015·The Journal of Chemical Physics·Patrick Smadbeck, Yiannis N Kaznessis
Feb 2, 2015·The Journal of Chemical Physics·M Núñez, D G Vlachos
Oct 24, 2017·Molecular BioSystems·Paola LeccaMarina Scarpa
Jan 4, 2007·Physical Biology·H Salis, Y N Kaznessis
Oct 16, 2009·Biotechnology Journal·Yiannis N Kaznessis
Apr 20, 2018·Frontiers in Computational Neuroscience·Tiina ManninenMarja-Leena Linne
Jul 12, 2018·Bulletin of Mathematical Biology·Minghan ChenYang Cao
Apr 8, 2011·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Yiannis N Kaznessis
Aug 22, 2006·Biophysical Journal·Jonathan Tomshine, Yiannis N Kaznessis

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Software Mentioned

G2
MPICH
MexCDF
Matlab
HyJCMSS
Hybrid
NetCDF
Hy3S NetCDF
TeraGrid
Linux

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