**SWOF Milestones and Deliverables**

1/21/2003

***Applications***

**Bob Wilhelmson (NCSA)**

-   Select target users for initial AG deployment (Done)

    -   NCAR Boulder CO (Joe Klemp and Bill Skamarock)

    -   NSSL Norman OK

    -   Kelvin Droegemeir, U of OK

    -   Possibly at MEAD members at Huntsville, AL and Rutgers
        University

    -   Lou Wicker at NSDL (?)

    -   NCSA

-   Establish multicast networking into each target site and office.
    (when?)

-   Acquire and deploy appropriate

    -   Access Grid (when?)

    -   GeoWall (Done, Jason?)

-   Deploy test version of AG 2.0 code with collaboration tools. (when?)

-   Acquire and test VIS5D streaming video application from ANL (when?)

-   Deploy VIS5D to participants (who?, when?)

-   Demonstrate all of the above at the All Hands Meeting

-   Evaluate impact, provide feedback to technology developers, review
    and redeploy next version. (when?)

-   Choose a VIZ app candidate for refactoring into a distributed app
    (when?)

-   Use AG 2.0 toolkit to refactor and deploy distributed viz app.
    (when?)

**Natalia Maltsev (ANL)**

-   Establish web-based access to metabolic and regulatory networks
    databases, being developed and maintained at MCS ANL. Specifically
    we will provide access to the following resources:

    -   Gwiz \-- a new generation of the web-based computational
        environment for high-throughput genetic sequence analysis and
        metabolic reconstructions from sequence data; (when?)

    -   public server of EMP database of Enzymes and Metabolic Pathways,
        and (when?)

    -   Sentra database of prokaryotic signal transduction proteins
        (when?)

-   Establish a prototype of the web-based public server for
    high-throughput genetic sequence analysis and automated assignment
    of functions to the genes. This server will provide assess to
    bioinformatics tools, including publicly available genetic sequence
    analysis tools developed by the other groups (Blast, FastA, Blocks,
    Pfam, CATH, etc.), as well as tools developed by Computational
    Biology group at MCS (voting algorithms for automated assignment of
    functions to genes, SVMMER, PhyloBlocks, etc) (when?)

-   Develop a prototype of a toolkit for visualization and analysis of
    metabolic and regulatory networks and will provide a web-based
    access to these tools. (when?)

-   Develop teaching materials on using these tools and databases for
    genome annotations and metabolic reconstructions in the framework of
    WIT. Provide web-based user-friendly interface for navigation,
    interactive analysis and representation of genomic data to the
    scientific community through the Gwiz server (when?)

**Nagiza F. Samatova (ORNL)**

-   Streamline access to metabolic and regulatory networks databases
    (WIT3, EMP, KEGG), sequence databases (NCBI, SwissProt/Trembl, TIGR,
    JGI), protein structure databases (PDB, SCOP) (when?)

-   Incorporate public genome sequence analysis tools, including genetic
    sequence analysis tools (Blast, FastA, Blocks, Pfam, etc.) and
    protein structure prediction tools (CATH, VAST, etc.). Develop
    teaching materials on using these visualization tools (when?)

-   Develop teaching materials on using these tools and databases for
    genome annotations and metabolic reconstructions in the framework of
    WIT. Provide web-based user-friendly interface for navigation,
    interactive analysis and representation of genomic data to the
    scientific community through the Gwiz server (when?)

-   Develop a prototype of new visualization tools for protein clusters
    and metabolic networks representation; integrate them into Genome
    analysis server framework. Develop and implement new tools for
    interactive analysis and display of metabolic and regulatory
    networks (when?)

**Eric Jakobsson (NCSA)**

-   Create Tiled display output for viewing and analysis of unrooted
    phylogenetic trees (TreeView, PHYLIP, PAUP) (when?)

-   Create Tiled Display output for viewing and analysis of Biomolecular
    Assemblies (VMD) (when?)

-   Create Tiled Display out put for viewing and analysis of sequence
    alignments (Clustall) (when?)

-   Utilize AG and Tiled Displays between Argonne and NCSA to visualize
    and analyze above output in collaborative sessions (when?)

-   Install High Throughput Genomics Server at NCSA Cluster (when?)

-   Give AG tutorial on use of the server (when?)

**Klaus Schulten (UIUC)**

-   Extend optimization of NAMD for Intel 64-bit architecture. (when?)

-   Adapt NAMD to TeraGrid global file and resource allocations systems.
    (when?)

-   Tune and evaluate NAMD potential as a distributed Teragrid
    application. (when?)

-   Port interactive molecular dynamics features of VMD and NAMD to
    support on-demand grid-based interactive simulations. (when?)

-   Couple NAMD to a quantum chemistry code as a grid-based application.
    (when?)

-   Maintain a BioCoRE server at NCSA. (when?)

-   Build a membrane systems portal using BioCoRE. (when?)

-   Assist the Grid development team to achieve interoperability between
    the BioCoRE portal and the Alliance portal. (when?)

-   Participate in relevant meetings and discussions. (when?)

***Technology***

**Sam Fulcomer (Brown University)**

-   Participation in service model design

-   Incorporation of OpenAL under Chromium (CrOpenAL)

-   Testing of CrOpenAL on TCASCV VR displays

-   Install and test Grid-based visualization services on TCASCV
    rendering and display resources

-   Design CrOpenAL server with OpenAL extensions, permitting compliance
    with Virtual Venue interface specification

-   Participation in development of Virtual Venue specification for
    3D/VR interfaces

-   Implementation and testing of CrOpenAL server

-   Installation and testing of Access Grid 3D and VR interface
    prototypes

-   Installation and testing of virtual computational molecular biology
    laboratory

-   Integration of CrOpenAL services with virtual computational
    molecular biology laboratory

**Jim Ahrens (LANL)**

-   Develop initial version of tiled-display rendering service using
    Chromium

-   Test and integrate Virtual Venue and Grid system services with
    rendering service; Develop initial versions of data management,
    visualization services using VTK, tailored to meet specific
    application community needs (Q2)

-   Initial version of visualization and rendering prototypes complete

-   Initial user testing and feedback

**Dave Semeraro (NCSA)**

-   Shared image whiteboard. Develop an application that will allow the
    user to share images with remote users. In addition a white board
    like overlay system will be provided that will enable interactive
    mark up of the images by all users. April 1 2003.

-   Shared animation system. Develop an application that will allow the
    user to share animations with remote collaborators. Shared control
    and synchronization will attempt to ensure that each participant
    will see the same frame at the same time and allow shared vcr type
    of playback and control. June 1, 2003.

-   Shared analysis and visualization system. Develop or adapt an
    existing analysis package for collaborative use in the AG
    environment. Candidate packages include VisAD, Vis5D, and
    applications based on NCAR Graphics. September 1, 2003

-   Move the VisBench application from a CORBA client/server application
    to a Grid services environment

-   Create a cluster based parallel visualization server to handle large
    data visualization problems.

-   Add collaborative capability to the VisBench application via the
    Grid based collaborative software infrastructure services that are
    being developed as part of this expedition.

-   Work with the scientific community to adapt VisBench client software
    to particular application area needs.

**Glen Breshnahan (Boston University)**

-   Publish documentation for all major AG software releases, including
    new enhancements and advanced visualization services, in close
    collaboration with appropriate developers

-   Coordinate technology transfer issues and interactions with PACS and
    EOT partners, participating in conference calls, meetings, and other
    activities

-   Encourage deployment of new technologies through AG Users Seminar
    Series

-   Provide AGDP overall vision and guidance

-   Maintain and update existing AGDP documents, including the Authors\'
    Guide

-   Develop, edit, and contribute to new AGDP documents and AG-in-a-Box
    web-based tutorials

-   Recruit members of appropriate development and target community
    groups to participate in the AGDP by authoring documents, and by
    serving on review and general support teams

-   Participate in scientific workspaces planning meetings and virtual
    venue discussions

-   Design 3D/VR navigation interface based on Virtual Venue interface
    specification; Participate in the visualization testbed

-   Development of 3D/VR navigation interface with Virtual Venue
    support; Participate in deployment and testing of Tiled Wall
    visualization components

-   Demonstrate integrated navigation and remote rendering using Virtual
    Venue service; Deploy end-to-end prototype of Grid-based data
    management, visualization and rendering

**Rick Stevens (ANL)**

-   Hold initial face-to-face SWOF expedition planning meeting followed
    by quarterly meetings (Done)

-   Design Virtual Venue based services for high-performance
    visualization, problem solving environments (?)

-   Select target visualization applications for atmospheric modeling
    and computational biology applications (Done)

-   Release Virtual Venue services interface model (latest May 03)

-   Conduct AG based quarterly expedition meeting (done, biweekly
    meeting starting)

-   Deploy initial Grid based visualization services for applications
    communities (?)

-   Test initial web based interface to the Access Grid (June 03)

-   Test Chromium based network visualization service from TeraGrid
    visualization server (?)

-   Release virtual venue interface specification for collaboration
    services, modality translation and 3D/VR interfaces (?)

-   Deploy initial Tiled Display remote visualization testbed and test
    interfaces to TeraGrid visualization servers (?)

-   Demonstrate 3Dand VR interfaces for the Access Grid

-   Conduct AG based quarterly expedition meeting (ongoing)

-   Demonstrate initial virtual computational molecular biology
    laboratory to target systems biology community including basic
    tools, directory services, initial databases and scientific datasets
    (November 03)

-   Demonstrate initial virtual atmospheric modeling and simulation
    laboratory to target UCAR community including basic tools, directory
    services, initial databases and scientific datasets (November 03)

**Tom DeFanti (UIC)**

-   Deployment/training for AGAVE systems at a number of sites (mid
    February 2003).

-   Deployment and Testing of TeraVision on a constrained number of
    sites to allow "walk-up and plug-in" distribution of laptop visuals
    (March 2003).

-   Deployment and Testing of voxel-based volume rendering on the AGAVE
    (March 2003).

-   Human factors experiments on use of tiled displays for increasing
    parallelism and group awareness between two sites (May 2003).

-   Deployment/training for AGAVE systems; High speed reliable multicast
    for broadcasting full resolution graphics

-   Deployment and Testing of TeraVision on a constrained number of
    sites to allow "walk-up and plug-in" distribution of laptop visuals;
    Deployment and Testing of voxel-based volume rendering on the AGAVE;
    Human factors experiments on use of tiled displays for increasing
    parallelism and group awareness between two sites

-   Deployment of TeraVision for broadcasting tiled visualizations
    between a limited number of sites (2-3). Human factors experiments
    on the coordination of multiple workspace interfaces- e.g. AG,
    AGAVE, Digital Touch Screen white boards, Tiled Displays

-   Remote volume rendering on the AGAVE. Testing of TeraVision for
    broadcasting tiled visualizations between a limited number of sites
    (2-3).