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Growing the Tree of Life at SDSC: Kick-Off Meeting. Mark A. Miller San Diego Supercomputer Center. OTHER SDSC/MULTI-SITE PROJECTS in BIOLOGY Alliance for Cell Signaling Encyclopedia of Life Joint Center for Structural Genomics Protein Data Bank Protein Kinase Resource

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Growing the tree of life at sdsc kick off meeting

Growing the Tree of Life at SDSC:Kick-Off Meeting

Mark A. Miller

San Diego Supercomputer Center

Scientific Community

View Providers

Tool Providers

Domain Scientists

  • Disciplinary Interfaces

    • Molecular Biology

    • Structural Biology

    • Algorithm developers







Computational Resources



Linux Clusters

“The GRID”




Informatics Center

Integrated Views




Tol project functions
TOL Project functions:

  • Algorithm development

  • Model development

  • Methodologies for model evaluation

  • Database methodologies

  • Software development

  • Scalability/High end computing

  • Integration technology

  • Education/outreach

Role of sdsc
Role of SDSC:

  • Unite the users with resources to do their science.

  • Create standards for the resource in partnership w/community.

  • Design a reference architecture that supports interoperability, evolvability, and extensibility.

  • Provide a common point of contact for project members and the community.

  • Create a resource that gives persistence to the work created under this funding.

For each project function we must ask
For each project function we must ask:

  • What are the overall goals?

  • What resources do we have presently?

  • Where is IT support limited?

  • What are the requirements for delivering on goals?

  • How can we formalize communication?

Of the project management we must ask:

  • How shall we prioritize the allocation of resources to goals?

    • How much effort to stabilize/wrap legacy SW (and which SW)?

    • What are trade offs of architectural specifications (SW and HW)?

    • What are the computational requirements (grid vs local) ?

    • What functions do we need to provide immediately?

    • What is the right mix of short term/long term investment?

Synergies features under development in other sdsc projects
Synergies: Features under development in other SDSC Projects

  • HEC (DataStar: IBM power4; 7 tf/ 235 GB memory; SunFire 12K)

  • Web/grid services (Blue Titan)

  • Workflows (Ptolemy II; Scitegic)

  • e-Notebook (partnership with Kinematik; internal efforts)

  • Molecular visualization tools (

  • Biological data federation (IBM DL federation;

  • )

Where do we start
Where do we start?

  • Create infrastructure that supports communication.

  • Create a specifications document/project plan for each functional area.

  • Map the specifications to existing resources; strategize around weaknesses.

  • Propose one or more architectures that map to the groups

  • needs.

Proposed timeline
Proposed timeline

  • November 2003 Inception:

    • possible architectures described.

    • requirements for systems identified

    • project planning and staffing,

    • Life Cycle Objectives documentation with at least one feasible system architecture.

  • February 2004 Elaboration:

    • System Software Architecture Description created.

    • Life Cycle Architecture review and commitment.

  • October 2004 Construction

    • Major coding of product occurs,

    • culminating in the delivery of "alpha" capability to the user together with documentation.

  • Sdsc tree of life team

    Mark Miller – Management/Logistics/Strategy

    David Stockwell – Data Base/Architecture

    Alex Borchers – Architecture/Data delivery tools/ User requirements

    Dana Jermanis – Graphic Art/Web Master

    SDSC Tree of Life Team

    SOAP Server

    Virtual community messaging

    XML/RDF store

    Metadata sharing

    BLAST Data

    Keyword data

    Stored queries


    Session info


    TOL Notebook

    Encyclopedia of Life

    SOAP Queries




    Keyword queries