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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
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+
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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