PRAGMA BioSciences Portal Raj Chhabra Susumu Date Junya Seo Yohei Sawai

PRAGMA BioSciences Portal

Raj Chhabra

Susumu Date

Junya Seo

Yohei Sawai

Integration of Portlets Make a Biosciences Portal

Easy to use of bioscience applications, easy to submit jobs to grid environment

Access through web browsers Don’t need to install some applications

with GridSphere Consists of …

Single Sing-on functions Access to bio-applications Grid portlets (managing grid environment) Meta-Scheduler

Grid Portlets Build upon the core features in the GridSphere portal

framework Provide developers with a framework for developing Grid

portals Offer developers a collection of "portlet services" for

performing tasks on the Grid Also provide a collection of simple, easy-to-use, well

integrated portlets that showcase the functionality offered in Grid Portlets These portlets include the core functionality every Grid portal should contain and can be used on their

own or in conjunction with custom Grid-enabled web applications

Single Sing-on based GAMA Grid Account Management Architecture (GAMA)

GAMA is complete GSI credential management and integration solution tailored for use in emerging CyberInfrastructure through web portals or web service-based clients

Make grid security as easy to use as any comercial web site while maintaining the security and delegation capabilities of GSI

Two components of GAMA GAMA Server

runs on secure, locked-down machine with no user accounts to increase security,

provides all services for user credential management through secure web services,

API support for creating new users, listing users and user authentication,

GAMA Portlets provides all administration and management functions for user

and administrator, provides facilities for users to request accounts and for

administrators to automate account approval process, supports GridSphere portal framework with no changes to the

core framework, allows multiple portals to connect to the same backend GAMA

server.

Meta-Scheduler CSF4

Community Scheduler Framework first GT4-WSRF compliant Meta-Scheduler CSF can communicate with other different Grid

environment Different Hardware, OS, Infrastructure, Local Scheduler,

Resource Manager…

CSF4 is a group of grid services host in GT4 Job submission, control, monitoring Queue Service for jobs

CSF4

GT2 LSF

GT4 PBS

GT4 SGE…

CSF4 Portlets

Portlets for CSF4 Provide easy use of CSF4 from interface

Creating job and submitting job Viewing job history and specifications Check job status Get the job output

Work in GridSphere Integrate with GridSphere & Grid Portlets Specify the CSF4 handle (local or remote) Use credentials generated with Grid Portlets

Collaborate with GAMA

CSF4 Portlets

CSF4

GridEnvironment

Access

Management

Access to Bio Applications Bio applications

Applications for Bio scientists Blast

Basic Local Alignment Search Tool Auto-Dock

Automated Docking Tool Namd

Molecular Dynamics Simulator

Grid Computing

Grid ComputingBioscienceApplication

(NAMD)

BioscienceApplication

(NAMD)

Client Bioscience portal

Molecular dynamics and NAMD

Molecular Dynamics(MD) A method to understand structure and function of

biomolecules Proteins, DNA, Membranes, and so on…

NAMD Parallel molecular dynamics code

Designed for high-performance simulationof large biomolecular systems

MD

Namd Portlets Portlets for NAMD

Provide easy use of NAMD from interface Uploading files

Used for simulation such as parameter file Creating configuration files

From uploaded files Setting an environment for simulation

Computing Resources, and so on Submitting jobs

Using Local Scheduler such as PBS

NAMD Portlets

Grid

Access

Management

GT4 PBS

NAMD

Uploading files

Creating configuration files

•Namd Portlets use local scheduler such as PBS•There is no portlet to use NAMD through CSF4⇒　 Creating portlet to use NAMD through CSF4

Submitting jobs

Created Portlet Portlet to use NAMD through CSF4

Using files from NAMD Portlets configuration file, parameters file, and so on

Setting parameters for CSF4 Job type, Delegation mode and so on

Submitting jobs with CSF4 Checking Job Status

NAMD Portlets

Grid

Access

CSF4

NAMD

Management

demo

School (QUT)

We studied at QUT.This is a photo of the room that we stayed.

This is a photo of when we were interviewed.Including our mate.

Activity

Language Exchange Activity

•With Japanese Association in QUT•Learn English and Teach Japanese•Make friends

Sightseeing

I could see the Koalas at the

Zoo (LonePine).

Also I enjoyed Koala Hug.

In the Zoo, there were also

Kangaroos.We can touch them freely.

I went to Fraser Island.

It was very beautiful sand Island.

Residence

Share House Sharing a house with other people

having your own room and sharing kitchen and bath

Two-story house with 8 rooms

Share Mates Chinese and Indian and Australian

and Japanese Multicultural experience

Memorable things

Beach Gold Coast and Sunshine Coast

Island Fraser island and Moreton island

Conclusion

Technical Experience Making bio science portal

GAMA CSF4 BioApplication (NAMD)

Cultural Experience Life in School Residence Sightseeing

Moving Forward

http://www.altair.com/ http://www.altair-india.com/