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

摘要: Motivation: Many important problems in cell biology require the dense nonlinear interactions between functional modules to be considered. The importance of computer simulation understanding cellular processes is now widely accepted, and a variety algorithms useful for studying certain subsystems have been designed. these are already used, large number models constructed on existing formalisms available. A significant computational challenge how we can integrate such sub-cellular running different types construct higher order models. Results: modular, object-oriented meta-algorithm based discrete-event scheduler Hermite polynomial interpolation has developed implemented. It shown that this new method efficiently handle many components driven by timescales. utility framework demonstrated further with 'composite' heat-shock response model combines Gillespie--Gibson stochastic algorithm deterministic differential equations. Dramatic improvements performance were obtained without accuracy drawbacks. multi-timescale demonstration coupled harmonic oscillators also shown. Availability: An implementation available as part E-Cell Simulation Environment Version 3 downloadable from http://www.e-cell.org/software. Benchmark included package, upon request. Supplementary information: Complete lists reactions parameters model, more results at http://www.e-cell.org/bioinfo/takahashi03-1-supp.pdf