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

Attila Kertesz, Ferenc Otvos, Peter 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 - Jul 2014

Keywords

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

ASJC Scopus subject areas

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

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