PRAGMA BioSciences Portal

1. PRAGMA BioSciences Portal Raj Chhabra Susumu Date Junya Seo Yohei Sawai

2. 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

3. 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

5. 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

6. 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.

9. 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 GT4 GT4 … LSF PBS SGE

10. 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 Access CSF4 Management Grid Environment

12. 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 Bioscience Application (NAMD) Bioscience portal Client

13. 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

14. 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 Access GT4 PBS Management Grid NAMD

15. Uploading files

16. Creating configuration files

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

18. 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 Access CSF4 Management Grid NAMD

20. demo

21. 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.

22. Activity Language Exchange Activity • With Japanese Association in QUT • Learn English and Teach Japanese • Make friends

23. Sightseeing In the Zoo, there were also Kangaroos. We can touch them freely. I went to Fraser Island. It was very beautiful sand Island. I could see the Koalas at the Zoo (LonePine). Also I enjoyed Koala Hug.

24. 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

25. Memorable things • Beach • Gold Coast and Sunshine Coast • Island • Fraser island and Moreton island

26. Conclusion • Technical Experience • Making bio science portal • GAMA • CSF4 • BioApplication (NAMD) • Cultural Experience • Life in School • Residence • Sightseeing

27. Moving Forward • http://www.altair.com/ • http://www.altair-india.com/