2005 AHM Planning: Visualization/Portal Working Group

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  • Morphometry BIRN: Anthony Kolasny
  • Function BIRN: Steve Pieper
  • Mouse BIRN: Ilya Zaslavsky
  • BIRN CC: Jason Novotny


  • Tuesday, October 18
    • 2:00pm - 3:15pm
    • An introduction to GridSphere
      • The portlet model allows for sites to do local development and also allow for the integration of these modules (i.e. portlets) into other compatible portlets
      • Portlet standards for community development (e.g. JSR-168)
    • 3:30pm - 4:45pm
    • The BIRN Portal Architecture
      • BIRN Portal Architecture allowing for centralized credential management and distributed development
      • BIRN Portal development environment, allowing for developers to test protal components against core services (e.g. SRB) in the staging environment
      • Discuss advancement of "Project" feature of the Portal for
        • Providing a "home" in the portal for individual projects to provide customized information to project members
        • Management of collaborative research projects

  • Wednesday, October 19
    • 8:30am - noon
    • Portal Use Cases and Requirements Gathering
      • What technologies should be incorporated to foster rapid collaborations
      • Portal applications (visualization, analysis, etc.) should be launchable regardless of the databases. There are several databases on the works (XNAT, HID, LONI-DB, etc.). Can a unified Portal interface deal with all?
      • Advanced and more intelligent methods for launching applications (e.g. portal "knowing" that a data set is a DICOM study and therefor can recommend viewers)
    • Afternoon
    • 'Working' Group Report
      • Summary report and a requirements document from the group will be presented to the whole BIRN group, outlining the milestones/dates/names agreed by the group.

Working Group Background Information

Background While computer technology is what makes it possible to conduct large-scale data analyses, most biologists are far more concerned and facile with their own field of science. Therefore, a critical activity area for BIRN is the development of an effective and intuitive interface to the BIRN cyberinfrastructure that facilitates and enhances the process of collaborative scientific discovery for the test bed participants. Ubiquitous access for all users has been accomplished by deploying the BIRN Portal, which:

  • Provides transparent and pervasive access to the BIRN cyber-infrastructure requiring only a single username and password;
  • Provides a scalable interface for users of all backgrounds and level of expertise;
  • Provides customized “work areas” that address the common and unique requirements of test bed groups and individual users;
  • Has a flexible architecture built on emerging software standards allowing for transparent access to sophisticated computational and data service; and
  • Requires a minimum amount of administrative complexity.

More than a simple Web interface, the BIRN Portal environment is designed to provide the integrated collection of tools, infrastructure, and services that BIRN test-bed researchers and databases users need access to in order to perform comprehensive and collaborative studies from any location with Internet access. The current production BIRN Portal is built upon the GridPort Toolkit (Thomas et al., 2001; Peltier et al., 2003), a collection of services developed that enable the creation of Web-based applications with secure and transparent access to grid infrastructure and resources. The BIRN-CC is currently transitioning the portal environment to GridSphere (http://www.gridsphere.org; Novotny et al., 2004), a leading open-source portlet environment. GridSphere will enable BIRN developers to quickly develop and package portlet web applications that can be run and administered within the GridSphere environment.

'Goals for the 2005 Portal/Visualization Working Group' This year’s AHM will focus on the transition from the current BIRN Portal architecture to GridSphere. Tuesday afternoon will focus on providing BIRN AHM participants with an overview of the GridSphere environment and the BIRN portal architecture. Wednesday morning will be focused on eliciting requirements and use cases from participants to help define the milestones and deliverables for the next 2 BIRN releases (3.0 – January 2006, 4.0 – July 2006).

Material to Review GridSphere Site http://www.gridsphere.org

GridSphere Architecture Overview http://www.gridsphere.org:80/gridsphere/wp-4/Slides/gridsphere/pdf/GridSphereOverview.pdf

UK e-Science GridSphere Workshop http://www.nesc.ac.uk/action/esi/contribution.cfm?Title=549

Publications GridSphere: A Portal Framework for Building Collaborations http://www.gridsphere.org/gridsphere/wp-4/Documents/RioBabyRio/gridsphere.pdf

GridSphere: An Advanced Portal Framework http://www.gridsphere.org/gridsphere/wp-4/Documents/France/gridsphere.pdf

Overview of JSR-168 (Java Portlet Standard) http://developers.sun.com/prodtech/portalserver/reference/techart/jsr168/

'Possible Participants at AHM'

  • Morphometry BIRN: Timothy Brown, Michael Bowers, Burak Ozyurt
  • Function BIRN: Steve Pieper, Nicole Aucoin, Wendy Plesniak, Burak Ozyurt, David Keator, Hans Johnson, Jeremy Bockholt (possibly)
  • Mouse BIRN: Josh Tran, Willy Wong, Steve Anderson, David Shattuck
  • BIRN CC: Jason Novotny, Thien Nguyen, Jana Nguyen, Ramil Manansala, Abel Lin, Mark James (part-time)

Links to BIRN tools