The Encyclopedia of Life Project Large Scale Gridenabled Proteome Annotation

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The Encyclopedia of Life ProjectLarge Scale
Grid-enabled Proteome Annotation

• Wilfred Li
• Integrative Biosciences
• San Diego Supercomputer Center
• UCSD

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Encyclopedia Of Life Project

• High quality functional and 3-D structure
  assignment using iGAP
• Grid-enabled bioinformatics applications
• Optimization
• Dedicated and external grid resources
• Integrative biological data warehouse
• Web services consumer
• Distributed database and data mining
• Advanced query environment
• Open Notebook
• Web services provider

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Tools

• Protein Annotation Toolbox
• A C library for structural annotation of
  proteins
• Integrative Genome Annotation Pipeline
• A wrapper for bioinformatics applications
• AppLeS Parameter Sweep Template
• A grid application environment
• Bioinformatics Workflow Management System
• A generic WMS for bioinformatics applications

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Protein sequences
structure info
sequence info
Prediction of signal peptides (SignalP,
PSORT) transmembrane (TMHMM, PSORT) coiled
coils (COILS) low complexity regions (SEG)
NR, PFAM
SCOP, PDB
Step 1
Building FOLDLIB PDB chains SCOP domains PDP
domains CE matches PDB vs. SCOP 90 sequence
non-identical minimum size 25 aa coverage (90,
gaps lt30, endslt30)

Structural assignment of domains by WU-BLAST
Step 2
Structural assignment of domains by PSI-BLAST
profiles on FOLDLIB
Step 3
Structural assignment of domains by 123D on
FOLDLIB
Step 4
Functional assignment by PFAM, NR assignments
FOLDLIB
Step 5
Domain location prediction by sequence
Step 6
Data Warehouse
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Growth of Non-Redundant (NR) Database
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SCOP Superfamily Distribution in Arabidopsis
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Coverage of Structural Information
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Grid Middleware
MDS/NWS/Ganglia
SCP/GASS/SRB/FTP
SSH/GRAM/GASS PBS/Loadleveler/Condor
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APST Software Architecture
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APST Support of Batch Resources
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BWMS
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Encyclopedia of Life A Global Collaborative
Project
BeSC
TiTech
CNIC
JLU
SDSC/US
BII
YMU/NTU
UFCG
MU
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Reassemble proteome, Data replication
iGAP Workflow
PAT-NR 1000 Genomes
Proteome Specific Benchmarking
iGAP Prestaging Execution Monitoring
Only unique sequences are processed
DBMS
iGAP WMS
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GridSpeed Architecture
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GridSpeed and EOL
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Data Storage
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Compute Hosts
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Application Information
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Defining Parameters
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GridMonitor
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EOL Workflow Web Interface
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EOL Book Interface
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EOL Workflow
BWMS
Users
36,164 proteins selected from 73 Proteomes
annotated during SC03
Status
Output
Tasks
Japst (Grail Lab)
Local Cluster
Grid Speed (Titech)
Prediction
Loading
Genome Database
GridMonitor (BII)
External Data Source
Web Services
Status update
Job Status Database
iGAP tasks
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EOL User Interfaces

• Workflow user interface
• Task distribution using APST (GRAIL lab, UCSD)
• Task submission from the web using GridSpeed
  (TiTech)
• Graphical interface to Job status database (BII)
• Job status database engine (SDSC)
• Annotation user interface
• Relational database backend
• Integration of additional resources
• Query session tracking
• Annotation quality validated in several studies
• iGAP user interface
• Java applications (jAPST)
• Command line
• For more info, visit http//eol.sdsc.edu

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PRAGMA Partners

• BII (Singapore)
• Grid middleware deployment
• Workflow web interface
• http//blast.bii-sg.org8090/eol/
• Resource sharing
• Viper cluster-BII
• Scientific Exchange
• Titech (Japan)
• Condor pool
• GridSpeed
• A grid portal environment for speedy deployment
  of applications
• http//www.gridspeed.org
• New partners
• Australia, Brazil, Ireland, China.

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SDSC/UCSD Partners

• Integrative Biosciences Department
• ROCKS
• Rocks 3.1 Grid Roll
• The EOL cluster
• http//saxicolous.sdsc.edu/ganglia/
• DAKS
• DataStar
• Advanced Database Laboratory
• SRB/Data Matrix
• UCSD
• Life Sciences Initiatives
• Campus collaborations

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Acknowledgement
Acknowledgement

• SDSC
• Fran Berman
• Director
• Philip E. Bourne
• 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

• SDSC
• Philip Papadoplous
• Rocks
• Mason Katz
• Greg Bruno
• Chaitan Baru
• David Archbell
• Adam Birnbaum
• UCSD
• Peter Arzberger
• PRAGMA
• Henri Casanova
• Jim Hayes
• Ceres Inc.
• Nickolai Alexandrov
• 123D
• Richard Flavell

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Acknowledgment

• BII, Singapore
• Larry Ang
• Kishore Sakharkar
• Arun Krishnan
• Atif Shahab
• Other BII members
• Titech, Japan
• Satoshi Matsuoka
• Toyotaro Suzumura
• Kouji Tanaka

• University of Monash, Australia
• David Abramson
• Colin Enticott
• Univ. Federal de Campina Grande, Brazil
• Zane Cirne,
• Eliane Cristina de Araujo
• Queen's University, UK
• Terence J Harmer
• David R Simpson