Transcript 0 PRAGMA Overview 19Nov08.ppt

PRAGMA
A Practical Collaborative Framework
IOIT-VN
Strengthen Existing and Establish
New Collaborations
Work with Science Teams to
Advance Grid Technologies and
Improve the Underlying
Infrastructure
http://www.pragma-grid.net
In the Pacific Rim and Globally
Working Groups: Organize Activities
Resources
Biosciences
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
HPC
Clusters,
NBCR,
TeraGrid,
MHPCC
Virtual
Directory Tree
/gfs/$USER
databases
applications
Zinc
NAMD
AutoDock
Oct 2008
Telescience
NCIDS
Gfarm File System
PRAGMA Portal
My WorkSphere
CSF4 Server
GEO
Mr. Bayes
PRIME Host and Mentor Sites
Research Apprenticeship; Cultural Experience
U Zurich
Switzerland
CNIC
China
Osaka U
Japan
UCSD
USA
U WI
USA
NCHC
Taiwan
UoHyd
India
USM
Malaysia
Monash U
Australia
U Auckland
U Waikato
New Zealand
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
Source Cindy Zheng
PRIUS and MURPA: Based on PRIME
New Models for Building Research Capacity and
Cultural Awareness
U Hyderabad +
Hyderabad, India
+
USM
Penang Malaysia
12 Oct 05
U Auckland
U Waikato
New Zealand
+
MURPA
31 Jul 08
Schedule
Tanaka, Yoshio
Abramson, David
Tatebe, Osamu
Kim, Namgyu
Shimojo, Shinji
Lin, Fang-Pang
Li, Wilfred
Tsai, Whey Fone
Date, Susumu
Miyanaga, Shoji
Abramson, David
Pham, Phillip
Han, Simon
Chu, Rachel
Tenedorio, Daniel
Resources
AIST
Resources
Monash
Interoperations
U Tsukuba
CSF4 and Gfarm
KISTI
eAIRS
Telescience
NICT/Osaka
Telescience
NCHC
EcoGrid/GLEON/CREON
Biosciences
UCSD/NBCR
Bioscience - Avian Flu Grid
GEO
NCHC
GEO WG, 3D GIS Taiwan project
Education
Osaka
Monash
UCSD
UCSD
UCSD
PRIUS
MURPA
PRIME
Identification of a Specific Inhibitor
Virtual Screening for SHP-2
3D Teleconferencing
Visit Our Booths
Member Institutions
AIST: National Institute for Advanced Industrial Science and Technology
CCS: Center for Computational Science, U Tsukuba
Cray
IST/CMC (Cybermedia Center) Osaka U
KISTI: Korea Institute for Science and Technology Information
NCHC: National Center for High-performance Computing
NCSA: National Center for Supercomputing Application
SDSC, Calit2, EVL: San Diego Supercomputer Center
Tokyo Tech
Collaborating Institutions
NCRR/NBCR/UCSD: National Center for Research Resources
NICT: National Institute for Information and Communications Technology
Booth
303
1551
532
2023
2511
1851
351
568
3208
3206
2908
Thanks
• National Center for High-performance
Computing
• National Applied Research Laboratory
• All PRAGMA Institutions and Collaborators
GLEON Sites
September 2008
Lake Erken, GLEON 7
September 2008
T. Blenckner
Understand lake dynamics at local, regional, global
scales through grassroots use of cyberinfrastructure
Lake Observatory
+
IT Development
Launched by PRAGMA
Telescience WG
GLEON 6, Florida
Source: Tim Kratz
Lake Sunapee, USA
Linking Data from Lakes Globally
Source: Tim Kratz
Typical Instrumentation
•Weather
•Thermistor
chain Finland
Ormajärven,
•Dissolved Oxygen sensor
Torrens Lake, Australia
•Chlorophyll
fluorometer
Yuan
Yang Lake,
•CDOM Taiwan
fluorometer
Lake Mangueira,
Brazil
•Turbidity
Lake Erken, Sweden
•pH
•CO2
•PAR penetration
Crystal Bog, USA
•ADCP
Lake Annie, USA
•etc
Lake Rotorua,
New Zealand
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
launched
Avian
Flu
Grid
• Slides
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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
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Acknowledgements
• Funding Agencies
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NSF
TATRC
NIH
Gordon and Betty Moore
Foundation
– Many others, see list in
PRAGMA Collaborative
Overview