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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

Growing the tree of life at sdsc kick off meeting

Growing the tree of life at sdsc kick off meeting

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?

Growing the tree of life at sdsc kick off meeting

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

    Growing the tree of life at sdsc kick off meeting

    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