Presentation on theme: "PRAGMA BioSciences Portal Raj Chhabra Susumu Date Junya Seo Yohei Sawai."— Presentation transcript:
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 Dont need to install some applications with GridSphere Consists of … Single Sing-on functions Access to bio-applications Grid portlets (managing grid environment) Meta-Scheduler
GridSphere Part of GridLab projects funded by EU 100% JSR168 compliant Open source & free to use Gridportlets- the most important offering of GridSphere project for Grid users Login, logout File upload & download (GridFTP based) Globus 2.4 based job submission Job monitoring Credential management (GSI based & MyProxy complaint) Profile personalization and Layout customization Administration portlets for creation of users, groups, portlet management and portal layout customization Persistence (using Hibernate)
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 Grid Environment 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 Bioscience Application (NAMD) Bioscience Application (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 simulation of large biomolecular systems MD
Molecular dynamics and NAMD(2/2) NAMD Parallel molecular dynamics code Designed for high-performance simulation of large biomolecular systems Use VMD for trajectory analysis VMD is a popular molecular graphics program Use of NAMD Couple files are needed Specifying parameters and so on Submitting these files to NAMD Get the results result
Molecular dynamics and NAMD(2/2) NAMD Parallel molecular dynamics code Designed for high-performance simulation of large biomolecular systems Use VMD for trajectory analysis VMD is a popular molecular graphics program
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
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
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