Transcript BioWG-update_Habibah&Wilfred

PRAGMA 10
Biosciences Working
Group Update
Habibah Wahab, Ph.D
Wilfred W. Li, Ph.D.
On behalf of
Karpjoo Jeong, Ph.D.
Key Activities
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Bioinformatics
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mpiBLAST-G2
 iGAP/Gfarm/CSF4
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Avian Flu Project
Metagenomics Annotation
Computational Chemistry
Biosciences Portal
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M*Grid
NCHC Portal
My WorkSphere
Telescience
AMEXg
 APAC portals
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Education and Training
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PRIME
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CNIC – Kai Nan, Zhong-hua
Lu
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University of Zurich
PRIUS
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Osaka University
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hosting 2 students from
UCSD on Avian flu projects
Kohei Ichikawa
Susumu Date
Summer Internship Program
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Jilin University
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Zhaohui Ding
Xiaohui Wei
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Publications
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[1] X. Wei, J. Jiang, W. W. Li, O. Tatebe, G. Xu, L. Hu, and J. Ju,
"Implementing Data Aware Scheduling and Data Management in Gfarm
using LSFtm Scheduler Plugin Mechanism," Future Generation of Computer
Systems, Submitted, 2006.
[2] X. Wei, Z. Ding, W. W. Li, O. Tatebe, J. Jiang, L. Hu, and P. W.
Arzberger, "Grid Infrastructure for Bioinformatics Applications Based on
CSF4," Future Generations of Computer Systems, Submitted, 2006.
[3] W. W. Li, S. Krishnan, K. Mueller, K. Ichikawa, S. Date, S. Dallakyan,
M. Sanner, C. Misleh, Z. Ding, X. Wei, O. Tatebe, and P. W. Arzberger,
"Building cyberinfrastructure for bioinformatics using service oriented
architecture," CCGrid 2006, Singapore, 2006.
[4] D. Abramson, A. Lynch, H. Takemaya, Y. Tanimura, S. Date, H.
Nakmura, K. Jeong, S. Hwang, J. Zhu, Z.-h. Lu, C. Amoreira, K. K.
Baldridge, H.-C. Lee, C.-W. Wang, H.-L. Shih, T. Molina, W. W. Li, and P. W.
Arzberger, "Deploying Scientific Applications to the PRAGMA Grid testbed:
Strategies and Lessons," CCGrid, Singapore, 2006.
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mpiBLAST-G2
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Protein sequences
structure info
sequence info
SCOP, PDB
NR, PFAM
Building FOLDLIB:
PDB chains
SCOP domains
PDP domains
CE matches PDB vs. SCOP
90% sequence non-identical
minimum size 25 aa
coverage (90%, gaps <30, ends<30)
FOLDLIB
Integrative Genome
Annotation Pipeline
(iGAP)
Prediction of :
signal peptides (SignalP, PSORT)
transmembrane (TMHMM, PSORT)
coiled coils (COILS)
low complexity regions (SEG)
Step 1
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
Step 5
Domain location prediction by sequence
Step 6
Data Warehouse
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Distributed analysis in a virtual
filesystem
Virtual Directory Tree
/gfarm/eol/apps
apps
igap
From Cluster-wide to Grid-wide environment
dbs
psiblast Foldlib NR
Gfarm File System
Transparent distributed data access and file affinity-based application scheduling
• Gfarm virtual filesystem
allows existing
application to utilize
distributed compute and
data resources
transparently and
efficiently.
• Applications such as
iGAP and their required
input data may be
automatically replicated
to each node on demand.
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PRAGMA Gfarm Testbed
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Taiwan
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 NCHC
 Academia
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USA
 AIST
 Titech
sinica
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 NCSA
 SDSC
 NBCR
Japan
Korea
 KISTI
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China
 CNIC
 JLU
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CSF4 integrate with Gfarm
 Gfarm
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Security
Share Secure Key
GSI Authentication
 User
certificate
 Delegate
 Proxy certificate
User credentials
CSF4
Frontend
Scheduler
A
Frontend
Scheduler
B
GFS
Mutual
Authentication
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Opal: Web Service Wrapper
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Opal WSRF Operation Provider
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M*Grid and e-Glyconjugates portal
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Reusable
components to
support a large
community
Comprehensive
environment for
molecular
simulation
studies
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Computational Chemistry
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Use of
Nimrod/G
Workflow
built with
web
services
Gemstone
Led by
Baldridge
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ASCC
IOIT-HCM
Upload
files/submit
jobs
Download
& view
User interface results
Hawk
Rocks-52
Aurora
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Real Science Applications
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Rational Drug Disovery of Novel Dengue Therapeutics.
Characterisation of drug binding site(s) on the DNA
Elucidating isoniazid resistance using Molecular Modelling Techniques.
Structure and function of PHA synthase Drug receptor database
Binding mode of andrographolide to Renin, HIV-1 Protease and Tyrosine
kinase enzymes.
Binding of erythromycin and its relatives to ribosome. Molecular Docking
and Molecular Dynamics Simulation Study.
Investigation of the Binding Properties of Some Flavonoids to Calcium
using Molecular Modelling Techniques.
Molecular Modelling of Cytochrome P450 2D6. Effects of Allelic variation
on the enzyme activity.
Structure based drug design of compounds derived from marine natural
products.
Chemical Reactivity as a Tool to Study Carcinogenicity: Reaction between
Estradiol and Estrone 3,4-Quinones Ultimate Carcinogens and Guanine.
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New Collaboration in the Fight
Against Avian Flu
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AIST (Japan), CNIC (China),
Konkook/KISTI (Korea),
UCSD/SDSC (USA), JLU
(China), CGPBRI (Univ.
Hawaii), USM (Malaysia)
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Solving real problems using
bioinformatics, molecular
simulation and grid tools
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IBM World Community Grid
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Avian Flu Proteome Annotation
and Analysis
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iGAP
 Rosetta
 MEME
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AutoDock
Amber
Gromacs
GAMESS
CHARMM
NAMD
Involve students and postdocs
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Pictures
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Participating Institutions
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SDSC/UCSD
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Jilin University
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Osamu Tatebe
Hiroshi Takemiya
Yusuke Tanimura
Satoshi Seikiguchi
Zhaohui Ding
Xiaohui Wei
Osaka University
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AIST
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Wilfred Li
Tomas Molina
Cindy Zheng
Peter Arzberger
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Konkuk
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Karpjoo Jeong
Taehoon Kim
Kookmin
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Susumu Date
Kohei Ichikawa
Shinji Shimojo
Suntae Hwang
Daeyong Heo
KISTI
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Jae-Hyuck Kwak
Young-Chul Hwang
APAC
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Rajesh Chhabra
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Participating Institutions
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USM
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Hurng-Chun Lee,
Chi-Wei Wang
Horng-Liang Shih
University of Zurich/SDSC
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Kim Baldridge
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Zhong-Hua Lu
Kai Nan
Bao Ping Yan
University of Wisconsin
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Fang-Pang Lin
Whey-Fone Tsai
Weicheng Huang
CNIC
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Santosh Mishra
Arun Krishnan
Academia sinica
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NCHC
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Habibah Wahab
Amin Malik Sah
Chan Huah Yong
BII
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Katherine (Trina) McMahon
Other Working Groups
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Mason Katz
Yoshio Tanaka
Shinji Shimojo
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Breakout Session Participants
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USM
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Drug and DNA interactions
Drug design
Wilfred Li
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Gfarm
Additional applications
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GAMESS
Gemstone
GAMESS/APBS hybrid pipeline
CNIC
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Xiaoming Zhang
Mimos
Mashkuri Yaacob
Irdawah Ab. Rahman
Kohei Ichikawa
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Web services
Susumu Date
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Bioportal, MPICH-G2, LCG,
Docking
EGEE
Osaka University
Kim Baldridge
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Hsin-Yen Chen
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UCSD/SDSC
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Habibah Wahab
Ahmad Yussof Hassan
Amin Malik Shah Abdul Majid
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ASCC
TDW
APAC
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Rajesh Chhabra
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Grid portals
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Portals
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Biosciences portal
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Wiki already set up
 PRAGMA wiki – http://auriga.qut.edu.au/pragma
 set up a PRAGMA portal and wiki
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AMEXg
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Link to all sites with available applications
Much details in VMD (KB)
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One way to install
Tiled Display
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For users to try
Could not see before
Gfarm testbed
Other technologies
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Communications
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Biosciences mailing list
 [email protected]
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msn, skype
Contact info listed.
Application stack
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APBS
Autodock
Amber
GAMESS
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Pipelines
Applications compiled for different architectures
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With examples
Central site
Complaints about heterogeneity of resources
Shared installations
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Avian flu Analysis
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Two projects planned for PRIME students at
CNIC
 Epitope identification
 Host selectivity
 Need synopsis to refine
collaborations and
subprojects
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Scientific discussion during breakout session –
PRAGMA 11
 Discuss
results
 Project coordination
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Metagenomics Annotation
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Sequencing of genomes from native
environmental samples
 Shared
software stack
 Routine analysis
 Use Gfarm/CSF4 for scheduling and data
replication
 Data services
 Portal (shared infrastructure)
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Supercomputing Demonstrations
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Potential Topics
display using VMD – Kim Baldrige
 BioPortal – Grid application portal
 CNIC demonstration – CNGrid
 GridSphere portal to Gfarm/CSF4
 Biosciences Portal.
 Tiled
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Booth Location
 SC04
-- KISTI
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Other Activities
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Summer interns
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Grant applications
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Applications from own funding agencies
Intellectual properties
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Australia: visa required
US: J-1 visa
International collaborations
Standard nondisclosure agreements
World community grid
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Philanthropic activities
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ISGC 2006 1~4 May Taipei
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EGEE Workshop
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Symposium
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Its purpose is to introduce the EGEE project, including its goals,
infrastructure, middleware and operations
It focuses on Grid core technology, Grid architecture, applications on
various domains such as High Energy Physics, Bio/Medical, Digital
Archive, and Atmospherics. World-Wide Grid application development,
infrastructure interoperation, and collaboration would also be discussed.
http://www.twgrid.org
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