A case study for biochemical application porting in european grids and clouds

Attila Kertesz, F. Ötvös, P. Kacsuk

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Researchers of various disciplines ranging from Life Sciences and Astronomy to Computational Chemistry create and use scientific applications producing large amount of complex data relying heavily on compute-intensive modeling, simulation, and analysis. Grid computing provides an efficient way for parallelizing and gridifying computational and data intensive applications of various research fields including molecular dynamics. In this paper, we examine a biochemical application that generates conformers by unconstrained molecular dynamics at high temperature to overcome conformational bias then finishes each conformer by simulated annealing and energy minimization to obtain reliable structures. We provide a general way for turning biochemical applications into scientific workflows that can be executed through Web-based portals exploiting the computational power of available distributed computing infrastructures such as production grids, clusters, supercomputers, or clouds. First, we describe the application porting process, then provide experimental results that show the achieved speed-up of the ported application on three different infrastructure; finally, we show how to design a more attractive and easily usable graphical interface for this application.

Original languageEnglish
Pages (from-to)1730-1743
Number of pages14
JournalConcurrency Computation Practice and Experience
Volume26
Issue number10
DOIs
Publication statusPublished - 2014

Fingerprint

Grid
Molecular Dynamics
Molecular dynamics
Infrastructure
Computational chemistry
Computational Chemistry
Scientific Workflow
Energy Minimization
Astronomy
Supercomputers
Life sciences
Grid computing
Supercomputer
Distributed computer systems
Grid Computing
Distributed Computing
Simulated annealing
Simulated Annealing
World Wide Web
Web-based

Keywords

  • application-specific portal
  • cloud computing
  • grid computing
  • molecular dynamics
  • TINKER library

ASJC Scopus subject areas

  • Computer Networks and Communications
  • Computer Science Applications
  • Software
  • Computational Theory and Mathematics
  • Theoretical Computer Science

Cite this

A case study for biochemical application porting in european grids and clouds. / Kertesz, Attila; Ötvös, F.; Kacsuk, P.

In: Concurrency Computation Practice and Experience, Vol. 26, No. 10, 2014, p. 1730-1743.

Research output: Contribution to journalArticle

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