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Large Scale Genome Analysis : From 3D Structural Prediction and Modeling to the Encyclopedia of Life (EOL)

Large Scale Genome Analysis : From 3D Structural Prediction and Modeling to the Encyclopedia of Life (EOL). Wilfred Li, Ph.D. Integrative Biosciences Program San Diego Supercomputer Center University of California, San Diego. Gene Annotation. Biochemical Pathway. Gene Expression

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Large Scale Genome Analysis : From 3D Structural Prediction and Modeling to the Encyclopedia of Life (EOL)

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  1. Large Scale GenomeAnalysis: From 3D Structural Prediction and Modelingto the Encyclopedia of Life (EOL) Wilfred Li, Ph.D. Integrative Biosciences Program San Diego Supercomputer Center University of California, San Diego

  2. Gene Annotation Biochemical Pathway Gene Expression Profile Nucleotide Sequence Amino Acid Sequence Gene Linkage 3-D Structure Chromosome Map

  3. EOL Components • High quality functional and 3-D structure assignment • Integrative biological data warehouse • Advanced query environment • A focus for future collaborative developments via the EOL Notebook • True API level integration with key biological resources

  4. Globus GRAM/GASS SSH/SCP Application Description PBS/Loadleveler/Condor SRB/SFTP Globus MDS/NWS/Ganglia Grid Metadata EOL and APST The AppLeS Parameter Sweep Template (APST) provides EOL with transparent access to Grid resources and smart scheduling via Grid middleware. EOL Software/Data Grid Resources A P S T

  5. Technology Push • A new 80 processor P4 2.2 GHz Linux cluster will be fully operational Oct. 7, 2002, with 1.3 Terabytes of file storage capacity, networked with gigabits connections and routers • set up by SDSC Rocks group • Part of PRAGMA pool • Access to NPACI 100 PC AMD Linux cluster at University of Michigan, expanded to 256 PC • Access to NPACI Blue Horizon (128 nodes, 8 processor/node) at SDSC, 5 Terabytes file storage system • Access to PRAGMA grid (Asia Pacific Bio Grid, > 256 processors) • Access to TeraGrid (US, > 3000 processors) • Grid middleware advancement

  6. Human Dictyostelium (slime mold) Collaboration with W. Loomis, Biology Dept. Helicobactor pylori (ulcer bacteria) C. elegans (Worm) Thermatoga (JCSG genome) Rice Collaboration with BGI Fugu (puffer fish) Collaboration with BII Waiting list Malaria (Oct. 10, 2002) Mouse Rat Pathogenic bacteria … EOL website http://pat.sdsc.edu http://eol.sdsc.edu Biology Pull

  7. SCOP Superfamily Distribution in Arabidopsis

  8. 1E6B: Glutathione S-Transferase

  9. SDSC Fran Berman Director Philip E. Bourne IBS Director Mark Miller Project Coordinator Ilya N. Shindyalov CE Greg Quinn Web service Coleman Mosley Vicente Reyes Robert Byrnes Kim Baldrige iCC Director Jerry Greenberg CE portal Philip Papadoplous Rocks Mason Katz Greg Bruno SDSC Chaitan Baru David Archbell Jerry Rowley UCSD Peter Arzberger PRAGMA Henri Casanova Jim Hayes Ceres Inc. Nickolai Alexandrov 123D Richard Flavell BII, Singapore Larry Ang Kishore Sakharkar Arun Krishnan Atif Shahab Other BII members Everyone else Additional partner institutions Acknowledgement

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