PRAGMA BioSciences Portal

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PRAGMA BioSciences Portal

• Raj Chhabra
• Susumu Date
• Junya Seo
• Yohei Sawai

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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

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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)

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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

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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

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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.

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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
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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
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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
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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
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Molecular dynamics and NAMD(2/2)

• NAMD
• Parallel molecular dynamics code
• Designed for high-performance simulationof 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

NAMD
result
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Molecular dynamics and NAMD(2/2)

• NAMD
• Parallel molecular dynamics code
• Designed for high-performance simulationof large
  biomolecular systems
• Use VMD for trajectory analysis
• VMD is a popular molecular graphics program

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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
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Uploading files
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Creating configuration files
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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

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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
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• demo

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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.
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Activity
Language Exchange Activity

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

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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.
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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

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Memorable things

• Beach
• Gold Coast and Sunshine Coast
• Island
• Fraser island and Moreton island

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Conclusion

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

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Moving Forward

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