Accelerating Exact Stochastic Simulation of Biochemical Systems

[1]  Jack Dongarra,et al.  MPI: The Complete Reference , 1996 .

[2]  C. Rao,et al.  Control, exploitation and tolerance of intracellular noise , 2002, Nature.

[3]  Krishnan Subramani,et al.  Analysis and Simulation of Mixed-Technology VLSI Systems , 2002, J. Parallel Distributed Comput..

[4]  Ami Marowka,et al.  The GRID: Blueprint for a New Computing Infrastructure , 2000, Parallel Distributed Comput. Pract..

[5]  John F. Keane,et al.  A compiled accelerator for biological cell signaling simulations , 2004, FPGA '04.

[6]  S. Shen-Orr,et al.  Network motifs in the transcriptional regulation network of Escherichia coli , 2002, Nature Genetics.

[7]  Catherine M Lloyd,et al.  CellML: its future, present and past. , 2004, Progress in biophysics and molecular biology.

[8]  Herbert M. Sauro,et al.  Bifurcation discovery tool , 2005, Bioinform..

[9]  Uri Alon,et al.  Efficient sampling algorithm for estimating subgraph concentrations and detecting network motifs , 2004, Bioinform..

[10]  C. Rao,et al.  Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm , 2003 .

[11]  R. Milo,et al.  Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[12]  E. Greenberg,et al.  The Vibrio fischeri quorum‐sensing systems ain and lux sequentially induce luminescence gene expression and are important for persistence in the squid host , 2003, Molecular microbiology.

[13]  Nagiza F. Samatova,et al.  Accelerating Exact Stochastic Simulation Using Reconfigurable Computing , 2005, ERSA.

[14]  R. Brent,et al.  Modelling cellular behaviour , 2001, Nature.

[15]  Michael Mascagni,et al.  SPRNG: A Scalable Library for Pseudorandom Number Generation , 1999, PP.

[16]  Tianhai Tian,et al.  A multi-scaled approach for simulating chemical reaction systems. , 2004, Progress in biophysics and molecular biology.

[17]  D. Gillespie.  Exact Stochastic Simulation of Coupled Chemical Reactions , 1977 .

[18]  M. L. Simpson,et al.  Frequency domain analysis of noise in autoregulated gene circuits , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[19]  Yiannis Kaznessis,et al.  Accurate hybrid stochastic simulation of a system of coupled chemical or biochemical reactions. , 2005, The Journal of chemical physics.

[20]  Lawrence F. Shampine,et al.  The MATLAB ODE Suite , 1997, SIAM J. Sci. Comput..

[21]  D. Gillespie.  The chemical Langevin equation , 2000 .

[22]  David R. Jefferson,et al.  Virtual time , 1985, ICPP.

[23]  Linda R Petzold,et al.  The slow-scale stochastic simulation algorithm. , 2005, The Journal of chemical physics.

[24]  E. Greenberg,et al.  Acyl-Homoserine Lactone Quorum Sensing in Bacteria , 2000 .

[25]  M. L. Simpson,et al.  Frequency domain analysis of noise in simple gene circuits. , 2006, Chaos.

[26]  D. Gillespie.  A rigorous derivation of the chemical master equation , 1992 .

[27]  D. Gillespie.  A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions , 1976 .

[28]  Lukasz Salwinski,et al.  In silico simulation of biological network dynamics , 2004, Nature Biotechnology.

[29]  D. Gillespie.  Approximate accelerated stochastic simulation of chemically reacting systems , 2001 .

[30]  Larry Lok.  The need for speed in stochastic simulation , 2004, Nature Biotechnology.

[31]  R. Strohman,et al.  Maneuvering in the Complex Path from Genotype to Phenotype , 2002, Science.

[32]  Ian Foster,et al.  The Grid 2 - Blueprint for a New Computing Infrastructure, Second Edition , 1998, The Grid 2, 2nd Edition.

[33]  Kevin Burrage,et al.  Stochastic approaches for modelling in vivo reactions , 2004, Comput. Biol. Chem..

[34]  M. Ptashne.  A genetic switch : phage λ and higher organisms , 1992 .

[35]  Chris D Cox,et al.  Analysis of noise in quorum sensing. , 2003, Omics : a journal of integrative biology.

[36]  Nagiza F. Samatova,et al.  The sorting direct method for stochastic simulation of biochemical systems with varying reaction execution behavior , 2006, Comput. Biol. Chem..

[37]  M. L. Simpson,et al.  Frequency domain chemical Langevin analysis of stochasticity in gene transcriptional regulation. , 2004, Journal of theoretical biology.

[38]  T. Elston,et al.  Stochasticity in gene expression: from theories to phenotypes , 2005, Nature Reviews Genetics.

[39]  H. Kurata,et al.  Feedback regulation of the heat shock response in E. coli , 2001, Proceedings of the 40th IEEE Conference on Decision and Control (Cat. No.01CH37228).

[40]  S. Ghosh,et al.  Simulating asynchronous, decentralized military command and control , 1996 .

[41]  A. Arkin,et al.  Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. , 1998, Genetics.

[42]  Michael A. Gibson,et al.  Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels , 2000 .

[43]  Brandon Parks Thurmon.  Reconfigurable Hardware Acceleration of Exact Stochastic Simulation , 2005 .

[44]  Francine Berman,et al.  Overview of the Book: Grid Computing – Making the Global Infrastructure a Reality , 2003 .

[45]  Henri Casanova,et al.  Netsolve: a Network-Enabled Server for Solving Computational Science Problems , 1997, Int. J. High Perform. Comput. Appl..

[46]  Hong Li,et al.  Efficient formulation of the stochastic simulation algorithm for chemically reacting systems. , 2004, The Journal of chemical physics.

[47]  Muruhan Rathinam,et al.  Stiffness in stochastic chemically reacting systems: The implicit tau-leaping method , 2003 .

[48]  Gregory D. Peterson,et al.  Accelerating Gene Regulatory Network Modeling Using Grid-Based Simulation , 2004, Simul..

[49]  K. Burrage,et al.  Binomial leap methods for simulating stochastic chemical kinetics. , 2004, The Journal of chemical physics.

[50]  Clifford A. Shaffer,et al.  The JigCell Model Builder and Run Manager , 2004, Bioinform..

[51]  R. M. Fujimoto,et al.  Parallel discrete event simulation , 1989, WSC '89.

[52]  Hiroaki Kitano,et al.  The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models , 2003, Bioinform..

[53]  Mark Kot,et al.  Elements of Mathematical Ecology: Frontmatter , 2001 .

[54]  R. Roy,et al.  Parallel discrete event simulation algorithm for manufacturing supply chains , 2004, J. Oper. Res. Soc..

[55]  Hideharu Amano,et al.  Stochastic Simulation for Biochemical Reactions on FPGA , 2004, FPL.

[56]  Linda R. Petzold,et al.  Improved leap-size selection for accelerated stochastic simulation , 2003 .

[57]  David McMillen,et al.  Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks , 2004, BMC Bioinformatics.

[58]  Mats Jirstrand,et al.  Systems biology Systems Biology Toolbox for MATLAB : a computational platform for research in systems biology , 2006 .

[59]  Faisal N. Abu-Khzam,et al.  On Special-purpose Hardware Clusters for High-performance Computational Grids , 2002, IASTED PDCS.