GridMACS portal: A grid web portal for molecular dynamics simulation using GROMACS

Elizabeth Chia, Mohd Shahir Shamsir, Zeti Azura Mohamed Hussein, Siti Zaiton Mohd Hashim

Research output: Chapter in Book/Report/Conference proceedingConference contribution

5 Citations (Scopus)

Abstract

We developed GridMACS, a grid-enabled web portal with the aim of providing GUI for GROMACS and running a molecular dynamics simulation in a grid environment. The portal is developed according to the basic grid system architecture by integrating the main grid layers such as the Gridsphere Portal Framework, Vine Toolkit (grid service) and Globus Toolkit (grid middleware). The integration with the computing resources was achieved by the deployment of the main grid layers on a cluster grid environment. Creation of this portal will provide a GUI based user-friendly environment that will assist biologist in providing them the availability and usability. GridMACS will serve as an initial proof of concept and in the future will subsequently become a platform for other bioinformatics tools to be implemented on a grid platform as a portlet application. The portal is easily accessible via the internet on any browsers at www.gridmacs.fbb.utm.my:8080/gridsphere/gridsphere.

Original languageEnglish
Title of host publicationAMS2010: Asia Modelling Symposium 2010 - 4th International Conference on Mathematical Modelling and Computer Simulation
Pages507-512
Number of pages6
DOIs
Publication statusPublished - 2010
EventAsia Modelling Symposium 2010: 4th International Conference on Mathematical Modelling and Computer Simulation, AMS2010 - Kota Kinabalu, Borneo
Duration: 26 May 201028 May 2010

Other

OtherAsia Modelling Symposium 2010: 4th International Conference on Mathematical Modelling and Computer Simulation, AMS2010
CityKota Kinabalu, Borneo
Period26/5/1028/5/10

Fingerprint

Grid Portal
Web Portal
Molecular Dynamics Simulation
Molecular dynamics
Grid
Computer simulation
Graphical user interfaces
Globus Toolkit
Grid Middleware
Bioinformatics
Middleware
Grid Service
System Architecture
Usability
Availability
Internet
Resources
Computing

Keywords

  • Globus Toolkit
  • Grid computing
  • Grid middleware
  • Grid service
  • Gridsphere
  • Gromacs
  • Molcular dynamics simulation
  • Vine Toolkit

ASJC Scopus subject areas

  • Applied Mathematics
  • Modelling and Simulation

Cite this

Chia, E., Shamsir, M. S., Mohamed Hussein, Z. A., & Mohd Hashim, S. Z. (2010). GridMACS portal: A grid web portal for molecular dynamics simulation using GROMACS. In AMS2010: Asia Modelling Symposium 2010 - 4th International Conference on Mathematical Modelling and Computer Simulation (pp. 507-512). [5489118] https://doi.org/10.1109/AMS.2010.103

GridMACS portal : A grid web portal for molecular dynamics simulation using GROMACS. / Chia, Elizabeth; Shamsir, Mohd Shahir; Mohamed Hussein, Zeti Azura; Mohd Hashim, Siti Zaiton.

AMS2010: Asia Modelling Symposium 2010 - 4th International Conference on Mathematical Modelling and Computer Simulation. 2010. p. 507-512 5489118.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Chia, E, Shamsir, MS, Mohamed Hussein, ZA & Mohd Hashim, SZ 2010, GridMACS portal: A grid web portal for molecular dynamics simulation using GROMACS. in AMS2010: Asia Modelling Symposium 2010 - 4th International Conference on Mathematical Modelling and Computer Simulation., 5489118, pp. 507-512, Asia Modelling Symposium 2010: 4th International Conference on Mathematical Modelling and Computer Simulation, AMS2010, Kota Kinabalu, Borneo, 26/5/10. https://doi.org/10.1109/AMS.2010.103
Chia E, Shamsir MS, Mohamed Hussein ZA, Mohd Hashim SZ. GridMACS portal: A grid web portal for molecular dynamics simulation using GROMACS. In AMS2010: Asia Modelling Symposium 2010 - 4th International Conference on Mathematical Modelling and Computer Simulation. 2010. p. 507-512. 5489118 https://doi.org/10.1109/AMS.2010.103
Chia, Elizabeth ; Shamsir, Mohd Shahir ; Mohamed Hussein, Zeti Azura ; Mohd Hashim, Siti Zaiton. / GridMACS portal : A grid web portal for molecular dynamics simulation using GROMACS. AMS2010: Asia Modelling Symposium 2010 - 4th International Conference on Mathematical Modelling and Computer Simulation. 2010. pp. 507-512
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