OCT 2009: HPC BioPortal for Singapore’s Local University

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

The authenticating and authorization are controlled via the university’s SVU (Active Directory) account. The portal can be accessed from outside but user needs to key in correct SVU username and password. The users can use all applications without further authentication after one time login.

The portal uses the SFTP protocol to communicate to background system. A web based file manager is implemented where users can explore the files and directories under their home directories. They can create, delete, modify, upload and download files to/from background file system from file manager web page.

The Portal provides a simple web interface to hide the complexity of users requiring the knowledge of Linux, LSF basic command as well as the applications’ commands and parameters when running a job manually.

There are 14 applications provided as listed according to the following categories:

Docking

• Autodock4

Modeling & Structure

• AMBER, Gaussian, MODELLER, NAMD, CHARMM, GROMACS

Phylogeny

• FastDNAml, Phase

Sequence Alignment & Analysis

• Clustalw-MPI, FastA, MAST, MEME, Muscle