A multi-algorithm, multi-timescale method for cell simulation Export

@article{citeulike:1218128, abstract = {Motivation: Many important problems in cell biology require the dense nonlinear interactions between functional modules to be considered. The importance of computer simulation in understanding cellular processes is now widely accepted, and a variety of simulation algorithms useful for studying certain subsystems have been designed. Many of these are already widely used, and a large number of models constructed on these existing formalisms are available. A significant computational challenge is how we can integrate such sub-cellular models running on different types of algorithms to construct higher order models. Results: A modular, object-oriented simulation meta-algorithm based on a discrete-event scheduler and Hermite polynomial interpolation has been developed and implemented. It is shown that this new method can efficiently handle many components driven by different algorithms and different timescales. The utility of this simulation framework is demonstrated further with a composite' heat-shock response model that combines the Gillespie-Gibson stochastic algorithm and deterministic differential equations. Dramatic improvements in performance were obtained without significant accuracy drawbacks. A multi-timescale demonstration of coupled harmonic oscillators is also shown. Availability: An implementation of the method is available as part of E-Cell Simulation Environment Version 3 downloadable from http://www.e-cell.org/software. Benchmark models are included in the package, and also available upon request. Supplementary information: Complete lists of reactions and parameters of the heat-shock model, and more results are available at http://www.e-cell.org/bioinfo/takahashi03-1-supp.pdf 10.1093/bioinformatics/btg442}, address = {Institute for Advanced Biosciences, Keio University, Fujisawa, Kanagawa, 252-8520, Japan.}, author = {Takahashi, Kouichi and Kaizu, Kazunari and Hu, Bin and Tomita, Masaru}, citeulike-article-id = {1218128}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btg442}, citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/20/4/538}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/14990450}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=14990450}, day = {1}, doi = {10.1093/bioinformatics/btg442}, issn = {1367-4803}, journal = {Bioinformatics}, keywords = {multi-formalism, multi-rate-simulation, multi-timescale, phd, system-biology}, month = {March}, number = {4}, pages = {538--546}, posted-at = {2009-08-20 06:25:50}, priority = {2}, title = {A multi-algorithm, multi-timescale method for cell simulation}, url = {http://dx.doi.org/10.1093/bioinformatics/btg442}, volume = {20}, year = {2004} }

TY - JOUR ID - citeulike:1218128 L3 - citeulike-article-id:1218128 N2 - Motivation: Many important problems in cell biology require the dense nonlinear interactions between functional modules to be considered. The importance of computer simulation in understanding cellular processes is now widely accepted, and a variety of simulation algorithms useful for studying certain subsystems have been designed. Many of these are already widely used, and a large number of models constructed on these existing formalisms are available. A significant computational challenge is how we can integrate such sub-cellular models running on different types of algorithms to construct higher order models. Results: A modular, object-oriented simulation meta-algorithm based on a discrete-event scheduler and Hermite polynomial interpolation has been developed and implemented. It is shown that this new method can efficiently handle many components driven by different algorithms and different timescales. The utility of this simulation framework is demonstrated further with a composite' heat-shock response model that combines the Gillespie-Gibson stochastic algorithm and deterministic differential equations. Dramatic improvements in performance were obtained without significant accuracy drawbacks. A multi-timescale demonstration of coupled harmonic oscillators is also shown. Availability: An implementation of the method is available as part of E-Cell Simulation Environment Version 3 downloadable from http://www.e-cell.org/software. Benchmark models are included in the package, and also available upon request. Supplementary information: Complete lists of reactions and parameters of the heat-shock model, and more results are available at http://www.e-cell.org/bioinfo/takahashi03-1-supp.pdf 10.1093/bioinformatics/btg442 IS - 4 JF - Bioinformatics SN - 1367-4803 AD - Institute for Advanced Biosciences, Keio University, Fujisawa, Kanagawa, 252-8520, Japan. EP - 546 TI - A multi-algorithm, multi-timescale method for cell simulation VL - 20 SP - 538 KW - multi-formalism KW - multi-rate-simulation KW - multi-timescale KW - phd KW - system-biology AU - Takahashi, Kouichi AU - Kaizu, Kazunari AU - Hu, Bin AU - Tomita, Masaru PY - 2004/03/01/ UR - http://dx.doi.org/10.1093/bioinformatics/btg442 ER -