Multilevel Modeling of Physiological Systems and Simulation Platform: PhysioDesigner, Flint and Flint K3 Service

Author

Asai, Yoshiyuki ; Abe, Takeshi ; Okita, Masao ; Okuyama, Tomohiro ; Yoshioka, Nobukazu ; Yokoyama, Shigetsohi ; Nagaku, Masaru ; Hagihara, Ken-ichi ; Kitano, Hiroaki

Author_Institution

OIST Grad. Univ., Okinawa, Japan

fYear

2012

fDate

16-20 July 2012

Firstpage

215

Lastpage

219

Abstract

Software framework to support modeling and performing simulations of multilevel physiological systems has been developed and expanded to support the cloud computing. The framework is composed of two blocks, i.e. PhysioDesigner and Flint. PhysioDesigner is an application providing a graphical user interface for assisting users in multilevel modeling of physiological functions and a terminal interface for script-based model building. Models built on PhysioDesigner are written in PHML (the physiological hierarchy markup language). Flint is a standalone simulator, supporting MPI for parallel computing on a proper system environment. Based on the standalone application, Flint K3 system supporting cloud computing has been developed, which provides a solution for portable high performance simulation. At the website of Flint K3, users can upload models described in PHML. In addition, PhysioDesigner and other applications can submit simulation jobs to Flint K3 directly at online.

Keywords

application program interfaces; biology computing; cloud computing; digital simulation; graphical user interfaces; message passing; parallel processing; software performance evaluation; Flint K3 service; MPI; PHML; PhysioDesigner; cloud computing; graphical user interface; multilevel modeling; multilevel physiological systems; parallel computing; physiological functions; physiological hierarchy markup language; portable high performance simulation; script-based model building; simulation platform; software framework; standalone simulator; terminal interface; user assistance; Biological system modeling; Computational modeling; Databases; Mathematical model; Numerical models; Physiology; Servers; cloud computing; integrated physiology; multilevel modeling; systems biology;

fLanguage

English

Publisher

ieee

Conference_Titel

Applications and the Internet (SAINT), 2012 IEEE/IPSJ 12th International Symposium on

Conference_Location

Izmir

Print_ISBN

978-1-4673-2001-6

Electronic_ISBN

978-0-7695-4737-4

Type

conf

DOI

10.1109/SAINT.2012.40

Filename

6305286