Paper Info
Title
Implementing a Space-Aware Stochastic Simulator on Low-Power Architectures: A Systems Biology Case Study
Abstract
In the last decade, different computing paradigms and modelling frameworks for the description and simulation of biochemical systems based on stochastic modelling have been proposed. From a computational point of view, many simulations of the model are necessary to identify the behaviour of the system. The execution of thousands of simulations can require huge amount of time, therefore the parallelization of these algorithms is highly desirable. In particular, models that consider the size of volumes and objects involved in the reaction are very time-consuming, since many rules should be considered to take into account the position of the different molecules. In this work we present an implementation of a stochastic space-aware simulator which exploits the benefit and features of hybrid low-power computing architectures. This work shows that the simulator dynamic probabilistic approach to select possible chemical reactions can be applied and implemented in hybrid low-power low-cost architectures as well as current industry high-end servers.
Year
DOI
Venue
2017
10.1109/PDP.2017.55
2017 25th Euromicro International Conference on Parallel, Distributed and Network-based Processing (PDP)
Keywords
Field
DocType
space-aware stochastic simulator,systems biology case study,biochemical systems,simulator dynamic probabilistic approach,hybrid low-power low-cost architectures
Computer science,Simulation,Parallel computing,Server,Systems biology,Exploit,Stochastic modelling,Probabilistic logic,Distributed computing
Conference
ISSN
ISBN
Citations 
1066-6192
978-1-5090-6059-7
2
PageRank 
References 
Authors
0.38
5
6
Name
Order
Citations
PageRank
Lucia Morganti1175.02
Elena Corni2103.65
Andrea Ferraro3143.27
Daniele Cesini4309.51
Daniele D'Agostino513023.39
Ivan Merelli629435.36