Strengthen Existing and Establish New Collaborations

Work with Science Teams to

Advance Grid Technologies and Improve the Underlying

Infrastructure

In the Pacific Rim and Globally

PRAGMA

http://www.pragma-grid.net

A Practical Collaborative Framework

IOIT-VN

Working Groups: Organize ActivitiesResources Biosciences

GEOTelescience

Gfarm File System

applications

databases

/gfs/$USER

NAMDAutoDock

Zinc NCIDS

Virtual Directory Tree

H5N1 related glycan conformation analysis

using M*Grid and Glyco-M*Grid

Relaxed Complex Method Molecular

Dynamics Simulation Data Sets & Database

Virtual Screening Data Sets & Database

PRAGMA PortalMy WorkSphere

CSF4 Server

HPC Clusters, NBCR,

TeraGrid, MHPCC

Mr. Bayes

Oct 2008

Currently there are 4 host sites: Osaka, NCHC, Monash, CNIC;New in 2008: USM, NTU, U Auckland, U Waikato, New 2009 U Hyderabad;

And new US mentoring sites: U WI

U ZurichSwitzerland

UoHydIndia

USMMalaysia

NCHCTaiwan

Monash UAustralia

U AucklandU Waikato

New Zealand

CNICChina

Source Cindy Zheng

U WIUSA

Osaka UJapan

PRIME Host and Mentor SitesResearch Apprenticeship; Cultural Experience

UCSDUSA

U AucklandU WaikatoNew Zealand

USMPenang Malaysia

U HyderabadHyderabad, India

+

+

+

12 Oct 05

31 Jul 08

PRIUS and MURPA: Based on PRIMENew Models for Building Research Capacity and

Cultural Awareness

MURPA

ScheduleResources

Tanaka, Yoshio AIST ResourcesAbramson, David Monash InteroperationsTatebe, Osamu U Tsukuba CSF4 and GfarmKim, Namgyu KISTI eAIRS

TelescienceShimojo, Shinji NICT/Osaka TelescienceLin, Fang-Pang NCHC EcoGrid/GLEON/CREON

BiosciencesLi, Wilfred UCSD/NBCR Bioscience - Avian Flu Grid

GEOTsai, Whey Fone NCHC GEO WG, 3D GIS Taiwan project

EducationDate, SusumuMiyanaga, Shoji Osaka PRIUSAbramson, David Monash MURPA

PRIME Pham, Phillip UCSD Identification of a Specific Inhibitor Han, Simon UCSD Virtual Screening for SHP-2 Chu, RachelTenedorio, Daniel UCSD 3D Teleconferencing

Visit Our Booths

Member Institutions BoothAIST: National Institute for Advanced Industrial Science and Technology 303CCS: Center for Computational Science, U Tsukuba 1551Cray 532IST/CMC (Cybermedia Center) Osaka U 2023KISTI: Korea Institute for Science and Technology Information 2511NCHC: National Center for High-performance Computing 1851NCSA: National Center for Supercomputing Application 351SDSC, Calit2, EVL: San Diego Supercomputer Center 568Tokyo Tech 3208

Collaborating InstitutionsNCRR/NBCR/UCSD: National Center for Research Resources 3206NICT: National Institute for Information and Communications Technology 2908

Thanks

• National Center for High-performance Computing

• National Applied Research Laboratory

• All PRAGMA Institutions and Collaborators

GLEON SitesSeptember 2008

Lake Observatory

+ IT Development

Source: Tim Kratz

Lake Erken, GLEON 7September 2008

T. Blenckner

GLEON 6, FloridaFebruary 2008

Launched by PRAGMATelescience WG

Understand lake dynamics at local, regional, globalscales through grassroots use of cyberinfrastructure

Lake Sunapee, USA

Lake Erken, Sweden

Yuan Yang Lake, Taiwan

Torrens Lake, Australia

Ormajärven, Finland

Lake Annie, USA Lake Rotorua, New Zealand

Crystal Bog, USA

Lake Mangueira,Brazil

Typical Instrumentation

•Weather

•Thermistor chain

•Dissolved Oxygen sensor

•Chlorophyll fluorometer

•CDOM fluorometer

•Turbidity

•pH

•CO2

•PAR penetration

•ADCP

•etc

Source: Tim Kratz Linking Data from Lakes Globally

Avian Flu Grid• Use PRAGMA Grid and

member technologies to construct and use international platform for screening and understanding avian flu

• Ten Institutions:– CNIC, Jilin U (China); AIST, U

Tsukuba (Japan); KISTI, Konkuk U (Korea); USM (Malaysia); Academia Sinica (Taiwan); U Hawaii, UCSD (US)

• Eight PRIME Students (two with publications)

• Improved codes:– data file systems, databases, grid

monitoring systems, algorithm for protein flexibility

• Identified promising compounds, being tested

• Funding from individual institutions, TATRC, NIH

• PRAGMA Biosciences WG launchedAvianFluGrid

Acknowledgements• Slides– Cindy Zheng– Wilfred Li– Tim Kratz– Ryosuke Nakamura– Shinji Shimojo– Larry Smarr– Paul Hanson– Tony Fountain– Sameer Tilak– David Abramson– Susumu Date– Fang-Pang Lin– Lily Cheng– …

• Funding Agencies– NSF– TATRC– NIH– Gordon and Betty Moore

Foundation– Many others, see list in

PRAGMA Collaborative Overview