HighThroughput Proteome Annotation in a Grid Portal Environment

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High-Throughput Proteome Annotation in a Grid
Portal Environment

• Steps towards routine use of the Grid
• Wilfred Li
• San Diego Supercomputer Center
• UCSD

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Growth of Non-Redundant (NR) Database
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Tools for Proteome Annotation

• 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
• Grid Portal Environment
• Interactive Use and Monitoring of Grid Resources

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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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Grid Middleware
MDS/NWS/Ganglia
SCP/GASS/SRB/FTP
SSH/GRAM/GASS PBS/Loadleveler/Condor
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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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GridSpeed Architecture
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EOL Workflow Web Interface
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EOL Book Interface
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EOL Workflow
BWMS
Users
Routine Use of the Grid, one genome at a time,
one resource at a time
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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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