PRAGMA BioSciences Portal Raj Chhabra Susumu Date Junya Seo Yohei Sawai
Mar 27, 2015
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
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