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APRIL 2013: NVG GEN 2 BioPortal

NovaGlobal has successfully completed a HPC Bioportal project with a university in Malaysia. The HPC Bioportal is a grid portal providing the web interface with Torque as the resource manager to access the bio-applications. It is running on the grid framework (Gridsphere) and developed by Java, JSP and JavaScript. Each application’s GUI is developed as a portlet on Portal.

The authenticating and authorization are controlled via Centralized Authentication System (LDAP) account. After the user logs on to the portal with the correct LDAP username and password, he or she is able to proceed using the applications without further authentication.

Secure FTP protocol is used to connect to Linux HPC cluster from the Portal system. The web based file manager is implemented and users can browse, create, delete, modify, upload, zip, unzip and download files/folder from file manager. Users can also monitor job statuses from the Job Manager and can view/download output from the file manager.

The portal provides a simple web interface and hides all the complexity at the background. User who wants to submit jobs from the Portal, they do not need to be familiar with Linux HPC and command line handling knowledge. Simple and user friendly web interfaces are provided for 14 applications.

The 14 applications provided are listed according to the following categories:

Docking
- Autodock4

Modeling & Structure
- AMBER, Gaussian, MODELLER, NAMD, GROMACS

Phylogeny
- FastDNAml, Phase

Sequence Alignment & Analysis
- Clustalw-MPI, FastA, MAST, MEME, Muscle