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PRAGMA 11 Biosciences Working Group Activities. Raj Chhabra Wilfred W. Li, Ph.D. Habibah Wahab, Ph.D. Metagenomics Bioinformatics, computational biology software Gfarm/CSF4 Avian Flu Project EGEE – Academia sinica UCSD Computational Chemistry Gemstone Biosciences Portals M*Grid

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Pragma 11 biosciences working group activities

PRAGMA 11 Biosciences Working Group Activities

Raj Chhabra

Wilfred W. Li, Ph.D.

Habibah Wahab, Ph.D


Key activities

Metagenomics

Bioinformatics, computational biology software

Gfarm/CSF4

Avian Flu Project

EGEE – Academia sinica

UCSD

Computational Chemistry

Gemstone

Biosciences Portals

M*Grid

NCHC Portal

My WorkSphere

APAC portals

Education and Training

PRIME – Avian Flu

CNIC – Kai Nan, Zhong-hua Lu

Lily Cheng and Lisa Zhao

PRIUS – Bioscience portal

Osaka University

Yohei Sawai

Sanyo Seo

Summer Interns -- Metascheduling

Jilin University

Zhaohui Ding

Yuan Luo

Xiaohui Wei

NBCR Summer Institute

Yoshio Tanaka -- AIST

Osamu Tatebe -- Tsukuba

Key Activities


Publications
Publications

  • [1] X. Wei, Z. Ding, W. W. Li, O. Tatebe, J. Jiang, L. Hu, and P. W. Arzberger, "GDIA: A Scalable Grid Infrastructure for Data Intensive Applications," presented at IEEE International Conference on Hybrid Information Technology, ICHIT 2006, Cheju Island, Korea, 2006.

  • [2] 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," presented at Sixth IEEE International Symposium on Cluster Computing and the Grid Workshops Singapore, 2006.

  • [3] Z. Ding, Y. Luo, X. Wei, C. Misleh, W. W. Li, P. W. Arzberger, and O. Tatebe, "My WorkSphere: Integrative Work Environment for Grid-unaware Biomedical Researchers and Applications," presented at Supercomputing Conference 2006, SC06, 2nd Grid Computing Environment Workshop, Tampa, Florida, 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," presented at Sixth IEEE International Symposium on Cluster Computing and the Grid, 2006. CCGrid 06., Singapore, 2006


Pragma gfarm testbed

Taiwan

NCHC

Academia sinica

USA

NCSA

SDSC

NBCR

Japan

AIST

Titech

Korea

KISTI

China

CNIC

JLU

PRAGMA Gfarm Testbed


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

New Collaboration in the Fight Against Avian Flu


Participating institutions

SDSC/UCSD (USA), JLU (China), CGPBRI (Univ. Hawaii), USM (Malaysia)

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

Participating Institutions


Participating institutions1

USM (USA), JLU (China), CGPBRI (Univ. Hawaii), USM (Malaysia)

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

Participating Institutions


Breakout session participants

USM (USA), JLU (China), CGPBRI (Univ. Hawaii), USM (Malaysia)

Habibah Wahab

Drug and DNA interactions

Drug design

UCSD/SDSC

Wilfred Li

Gfarm

Additional applications

Kayo Arima

metagenomics

NCHC

Chang-huain Hsieh

HPC – Fruitfly brain project

Ye-Nu Wan

SGI

Hideaki Shoda – Sponsor

Hiroaki Kondo

FLU

Julio Ibavre

ASCC

Hsin-Yen Chen

Bioportal, MPICH-G2, LCG, Docking

EGEE

Osaka University

Kohei Ichikawa -- Web services

Susumu Date

Portal

Junya Seo

Yohei Sawai

APAC

Rajesh Chhabra -- Bioportals

JLU

Xiaohui Wei -- CSF4

Senri-I (Senri Inter. Infor. Inst).

Ryiuchi Shimizu

U Canterbury

Neil Gemmell

U Auckland

Paul Bonnington

Breakout Session Participants


Portals
Portals (USA), JLU (China), CGPBRI (Univ. Hawaii), USM (Malaysia)

  • 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


Communications
Communications (USA), JLU (China), CGPBRI (Univ. Hawaii), USM (Malaysia)

  • Biosciences mailing list

    • [email protected]

    • 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


Avian flu analysis
Avian flu Analysis (USA), JLU (China), CGPBRI (Univ. Hawaii), USM (Malaysia)

  • Two projects planned for PRIME students at CNIC

    • Neuraminidase inhibitor

    • Host selectivity

    • Need synopsis to refine collaborations and subprojects

  • Scientific discussion during breakout session – PRAGMA 11

    • Discuss results

    • Project coordination


Metagenomics annotation
Metagenomics Annotation (USA), JLU (China), CGPBRI (Univ. Hawaii), USM (Malaysia)

  • 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)


Supercomputing demonstrations
Supercomputing Demonstrations (USA), JLU (China), CGPBRI (Univ. Hawaii), USM (Malaysia)

  • Potential Topics

    • Tiled display using VMD – Kim Baldrige

    • BioPortal – Grid application portal

    • CNIC demonstration – CNGrid

    • GridSphere portal to Gfarm/CSF4

    • Biosciences Portal.

  • Booth Location

    • SC06 – Osaka/UCSD


Other activities
Other Activities (USA), JLU (China), CGPBRI (Univ. Hawaii), USM (Malaysia)

  • Summer interns

    • Australia: electronic business visa (up to 90 days) no hassle

    • US: J-1 visa

  • Grant applications

    • Applications from own funding agencies

  • Intellectual properties

    • International collaborations

    • Standard nondisclosure agreements

  • World community grid

    • Philanthropic activities


Discussion points
Discussion points (USA), JLU (China), CGPBRI (Univ. Hawaii), USM (Malaysia)

  • What is available?

    • BioSciences Portal –Osaka/UCSD/APAC initial stage

    • Autodock Portal – Taiwan- testing stage

    • Many other portals & tools –displayed in past

  • Important to know how to use them

    • What are the requirements

    • Can PRAGMA members use those? Licensing etc?


Discussion points1
Discussion points.. (USA), JLU (China), CGPBRI (Univ. Hawaii), USM (Malaysia)

  • Different users want different software

    • Autodock /dock

    • UIUC’s NAMD

  • Lets extends the BioSciences portal to have a Molecular Dynamics suite

  • Having students is a great help

    • Need to be around for 4-6months

    • 2 months simply fly


Next 6 months
Next 6 months (USA), JLU (China), CGPBRI (Univ. Hawaii), USM (Malaysia)

  • Resources group

    • Getting software stack deployed on PRAGMA resources, NAMD, Autodock, dock

    • CA IGTF recognized

    • New policy for deploying GAMA based authentication

  • What researchers want?

    • Written wishlists from researchers/institute –on the wiki (to keep it dynamic)


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