کد مقاله کد نشریه سال انتشار مقاله انگلیسی نسخه تمام متن
421527 684877 2015 19 صفحه PDF دانلود رایگان
عنوان انگلیسی مقاله ISI
HSIM: A Hybrid Stochastic Simulation System for Systems Biology
موضوعات مرتبط
مهندسی و علوم پایه مهندسی کامپیوتر نظریه محاسباتی و ریاضیات
پیش نمایش صفحه اول مقاله
HSIM: A Hybrid Stochastic Simulation System for Systems Biology
چکیده انگلیسی

This paper describes a method to obtain in a certain sense the best of two well known simulation approaches: Stochastic simulation of chemical reactions and Entity-centered (multi-agents) systems. The stochastic simulation algorithm and its enhanced versions are adapted to simulate the behaviour of well stirred mixture of reactants when spatial localisation is not relevant; Conversely, in entity-centered methods, the causes and consequences due to spatial localisation are well handled. In terms of computational efficiency, the SSA methods are limited by the number of reactions and not by the amount of reactants, whereas it is the opposite for the entity-centered method. We will show how we can benefit from each approach, and also propose a new optimised algorithm for approximate stochastic simulation.

ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Electronic Notes in Theoretical Computer Science - Volume 313, 6 May 2015, Pages 3-21