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


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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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Large scale genome analysis from 3d structural prediction and modeling to the encyclopedia of life eol

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


Gene annotation

Gene Annotation

Biochemical

Pathway

Gene Expression

Profile

Nucleotide

Sequence

Amino Acid

Sequence

Gene

Linkage

3-D Structure

Chromosome

Map


Eol components

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


Large scale genome analysis from 3d structural prediction and modeling to the encyclopedia of life eol

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


Technology push

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


Biology pull

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


Scop superfamily distribution in arabidopsis

SCOP Superfamily Distribution in Arabidopsis


1e6b glutathione s transferase

1E6B: Glutathione S-Transferase


Acknowledgement

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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