University Technology Malaysia

Project details
Project details: 

GridMACS Portal is a portal for Molecular Dynamics Simulation for GROMACS with Globus Toolkit (GT4) middleware and SGE job scheduler. It is a grid-enabled web portal with the aim of providing GUI for GROMACS and running a molecular dynamics simulation in a 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 http://www.gridmacs.fbb.utm.my:8080/gridsphere/gridsphere.

Usecase for Vine: 

Vine is used for its credential, file and job manager. An addition to the job manager that had been included is the Upload button where users have the option of using the File Popup Browser instead of the previous option which only allowed filling in the details on the field provided. The popup file browser adds usability to the portal.

Basic use case:
1. user keys in passphrase at credential manager.
2. user goes to job manager and submits a simulation job by specifying (or selecting from file browser) executables needed to run simulation.
3. user is able to check job status from job listing on job manager.
4. user can obtain output files from file manager and download/delete them.

Contact information
Submitter: 
Elizabeth Chia