PRAGMA 10 Biosciences Working Group Update

Habibah Wahab, Ph.DWilfred W. Li, Ph.D.On behalf of Karpjoo Jeong, Ph.D.

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Key Activities

Bioinformatics mpiBLAST-G2 iGAP/Gfarm/CSF4

Avian Flu Project Metagenomics Annotation Computational Chemistry Biosciences Portal

M*Grid NCHC Portal My WorkSphere Telescience AMEXg APAC portals

Education and Training PRIME

CNIC – Kai Nan, Zhong-hua Lu

hosting 2 students from UCSD on Avian flu projects

University of Zurich PRIUS

Osaka University Kohei Ichikawa Susumu Date

Summer Internship Program Jilin University

Zhaohui Ding Xiaohui Wei

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Publications

[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

Prediction of : signal peptides (SignalP, PSORT) transmembrane (TMHMM, PSORT) coiled coils (COILS) low complexity regions (SEG)

Structural assignment of domains by PSI-BLAST profiles on FOLDLIB

Structural assignment of domains by 123D on FOLDLIB

Structural assignment of domains by WU-BLAST

Data Warehouse

Functional assignment by PFAM, NR assignments

FOLDLIB

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)

Domain location prediction by sequence

structure info sequence info

Step 1

Step 2

Step 3

Step 4

Step 5

Step 6

NR, PFAMSCOP, PDB

Integrative Genome Annotation Pipeline(iGAP)

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• 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.

Distributed analysis in a virtualfilesystem

Gfarm File System

/gfarm/eol/apps

igap psiblast Foldlib NR

Virtual Directory Tree

Transparent distributed data access and file affinity-based application scheduling

From Cluster-wide to Grid-wide environmentapps dbs

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PRAGMA Gfarm Testbed

Taiwan NCHC Academia sinica

USA NCSA SDSC NBCR

Japan AIST Titech

Korea KISTI

China CNIC JLU

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CSF4

CSF4 integrate with Gfarm

Gfarm Security Share Secure Key GSI Authentication

User certificate DelegateProxy certificate

User credentials

FrontendScheduler

A

FrontendScheduler

B

Mutual Authentication

GFS

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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

Reusable components to support a large community

Comprehensive environment for molecular simulation studies

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Computational Chemistry

Use of Nimrod/G

Workflow built with web services

Gemstone Led by

Baldridge

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User interface

Hawk

Rocks-52

ASCC

Aurora

IOIT-HCM

Gsiftp

inpu

ts &

resu

ltsGlo

bus-

subm

it

jobs

Gsiftp inputs &

results

Globus-submit jobs

Gsiftp inputs & resultsGlobus-submit jobs

Gsiftp inputs &

results

Globus-subm

it jobs

Upload files/submit jobs

Download & view results

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Real Science Applications 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 AIST (Japan), CNIC (China),

Konkook/KISTI (Korea), UCSD/SDSC (USA), JLU (China), CGPBRI (Univ. Hawaii), USM (Malaysia) IBM World Community Grid

Avian Flu Proteome Annotation and Analysis iGAP Rosetta MEME

Involve students and postdocs

Solving real problems using bioinformatics, molecular simulation and grid tools AutoDock Amber Gromacs GAMESS CHARMM NAMD

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Pictures

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Participating Institutions

SDSC/UCSD Wilfred Li Tomas Molina Cindy Zheng Peter Arzberger

AIST Osamu Tatebe Hiroshi Takemiya Yusuke Tanimura Satoshi Seikiguchi

Jilin University Zhaohui Ding Xiaohui Wei

APAC Rajesh Chhabra

Osaka University Susumu Date Kohei Ichikawa Shinji Shimojo

Konkuk Karpjoo Jeong Taehoon Kim

Kookmin Suntae Hwang Daeyong Heo

KISTI Jae-Hyuck Kwak Young-Chul Hwang

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Participating Institutions

USM Habibah Wahab Amin Malik Sah Chan Huah Yong

BII Santosh Mishra Arun Krishnan

Academia sinica Hurng-Chun Lee, Chi-Wei Wang Horng-Liang Shih

University of Zurich/SDSC Kim Baldridge

NCHC Fang-Pang Lin Whey-Fone Tsai Weicheng Huang

CNIC Zhong-Hua Lu Kai Nan Bao Ping Yan

University of Wisconsin Katherine (Trina) McMahon

Other Working Groups Mason Katz Yoshio Tanaka Shinji Shimojo

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Breakout Session Participants

USM Habibah Wahab Ahmad Yussof Hassan Amin Malik Shah Abdul Majid

Drug and DNA interactions Drug design

UCSD/SDSC Wilfred Li

Gfarm Additional applications

Kim Baldridge GAMESS Gemstone GAMESS/APBS hybrid pipeline

CNIC Xiaoming Zhang

ASCC Hsin-Yen Chen

Bioportal, MPICH-G2, LCG, Docking

EGEE Mimos Mashkuri Yaacob Irdawah Ab. Rahman

Osaka University Kohei Ichikawa

Web services Susumu Date

TDW APAC

Rajesh Chhabra Grid portals

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Portals

Biosciences portal Wiki already set up PRAGMA wiki – http://auriga.qut.edu.au/pragma set up a PRAGMA portal and wiki

For users to try AMEXg

One way to install Link to all sites with available applications

Tiled Display Much details in VMD (KB)

Could not see before Gfarm testbed Other technologies

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Communications

Biosciences mailing list

pragma-biosciences@pragma-grid.org msn, skype Contact info listed.

Application stack APBS Autodock Amber GAMESS

Pipelines Applications compiled for different architectures

With examples Central site Complaints about heterogeneity of resources Shared installations

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Avian flu Analysis

Two projects planned for PRIME students at CNIC Epitope identification Host selectivity Need synopsis to refine collaborations and

subprojects Scientific discussion during breakout session –

PRAGMA 11 Discuss results Project coordination

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Metagenomics Annotation

Sequencing of genomes from native environmental samples Shared software stackRoutine analysisUse Gfarm/CSF4 for scheduling and data

replicationData servicesPortal (shared infrastructure)

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Supercomputing Demonstrations

Potential TopicsTiled display using VMD – Kim BaldrigeBioPortal – Grid application portalCNIC demonstration – CNGridGridSphere portal to Gfarm/CSF4Biosciences Portal.

Booth LocationSC04 -- KISTI

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Other Activities

Summer interns Australia: visa required US: J-1 visa

Grant applications Applications from own funding agencies

Intellectual properties International collaborations Standard nondisclosure agreements

World community grid Philanthropic activities

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ISGC 2006 1~4 May Taipei

EGEE Workshop Its purpose is to introduce the EGEE project, including its goals,

infrastructure, middleware and operations Symposium

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