CAMPUS GRID WORKSHOP, ICT RESEARCH PLATFORM, 16 MAY 2007 PRAGMA : My personal hope & future Habibah...
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Transcript of CAMPUS GRID WORKSHOP, ICT RESEARCH PLATFORM, 16 MAY 2007 PRAGMA : My personal hope & future Habibah...
CAMPUS GRID WORKSHOP , ICT RESEARCH PLATFORM, 16 MAY 2007
PRAGMA : My PRAGMA : My personal hope & personal hope & futurefuture Habibah A Wahab, School of Pharmaceutical Sciences,Universiti Sains Malaysia
CAMPUS GRID WORKSHOP , ICT RESEARCH PLATFORM, 16 MAY 2007
PRAGMA: INVOLVEMENT BY CHANCE
• 2001 – 27th Aug: Presenting TB work in American Chemical
Society Meeting– 28th Aug: Invited to present seminar in Institute for TB
Research, Univ. Illinois in Chicago – 29th Aug : Visited San Diego Supercomputer Center – Met
fellow computational scientists – Dr. Kim Baldridge– Oct: Invited to join the first Malaysian Top Down Grant
on Grid Research – to work on Molecular Docking.• 2002
– Jan: P. Arzberger invited USM to join the Inaugral PRAGMA meeting.
– Chan Huah Yong to present Grid Research Group– Habibah to attend as observer.
CAMPUS GRID WORKSHOP , ICT RESEARCH PLATFORM, 16 MAY 2007
UNIVERSITI SAINS MALAYSIA AND PRAGMA: 2002
•Penang Bridge metaphorically presented to bridge USM & SDSC in grid computing
•Working group was established – USM to join resource working group
•Already decided not to involve in Grid/PRAGMA
•Did not attend PRAGMA 2.
CAMPUS GRID WORKSHOP , ICT RESEARCH PLATFORM, 16 MAY 2007
PRAGMA’s MISSION
• Among a community of investigators in the Pacific Rim– Establish sustained collaborations – Advance the use of the grid
technologies in scientific applications
CAMPUS GRID WORKSHOP , ICT RESEARCH PLATFORM, 16 MAY 2007
USM & PRAGMA
• Commitment to PRAGMA’s Mission– Sharing of resources: USM contributes a total of 34
nodes (51 cpus) to PRAGMA’s test-bed. – Host PRAGMA’s meeting – All are welcome to PRAGMA
15. 22-24th October, 2008 in USM’s main campus, Penang, Malaysia.
– Real Grid Applications: AutoDock on the Grid, AMEXg, AMBER in Gfarm
– Participate in PRIUS’s lectures– Accept 3 PRIUS students to do attachment in USM –
NADI-VISAGE (AutoDock & Dock)– Involve in Avian Flu Grid
• (SBDD Avian Flu Chemotherapeutic: RM 1mil for 3 years)
CAMPUS GRID WORKSHOP , ICT RESEARCH PLATFORM, 16 MAY 2007
CAMPUS GRID WORKSHOP , ICT RESEARCH PLATFORM, 16 MAY 2007
CAMPUS GRID WORKSHOP , ICT RESEARCH PLATFORM, 16 MAY 2007
CAMPUS GRID WORKSHOP , ICT RESEARCH PLATFORM, 16 MAY 2007
BIOSCIENCE
CAMPUS GRID WORKSHOP , ICT RESEARCH PLATFORM, 16 MAY 2007
CAMPUS GRID WORKSHOP , ICT RESEARCH PLATFORM, 16 MAY 2007
PRAGMA Grid TestbedPRAGMA Grid Testbed
AIST, JapanCNIC, China
KISTI, Korea
ASCC, Taiwan
NCHC, TaiwanUoHyd, India
MU, Australia
BII, Singapore
KU, Thailand
USM, Malaysia
NCSA, USA
SDSC, USA
CICESE, Mexico
UNAM, Mexico
UChile, Chile
TITECH, Japan
CAMPUS GRID WORKSHOP , ICT RESEARCH PLATFORM, 16 MAY 2007
PRAGMA Grid Resources
http://pragma-goc.rocksclusters.org/pragma-doc/resources.html
CAMPUS GRID WORKSHOP , ICT RESEARCH PLATFORM, 16 MAY 2007
PRAGMA’s gathering old & new….• PRAGMA 1 March, 2002 at the San Diego Supercomputer Center at the University
of California at San Diego. • PRAGMA 2 Seoul, Korea, Korea Institute of Science and Technology Information
(KISTI). • PRAGMA 3, Fukuoka, Japan - January 2003, AIST & Osaka U• PRAGMA 4, Melbourne, Australia, June 2003, APAC • PRAGMA 5 , Taipei, Taiwan, October 2003, NCHC • PRAGMA 6, Beijing, China, May, 2004, Chinese Academy of Science (CNIC) • PRAGMA 7, SDSC, September 15-17, 2004 (SDSC)• PRAGMA 8, Singapore, May 2005, BII and National Grid Office (Singapore). • PRAGMA 9, Hyderabad, October 2005, University of Hyderabad in Hyderabad,
India. • PRAGMA 10, Townsville, Queensland, Australia in March 2006, APAC, Monash U• PRAGMA 11 Osaka, Japan October 15-18, 2006, Osaka U.• PRAGMA 12 Bangkok, Thailand, March 20-22, 2007, Kasertsart U, Thai Grid Office.• PRAGMA 13 Urbana-Champaign, IL (USA), September 23-25, 2007, NCSA.• PRAGMA 14, Spring 2008, National Center for High-performance Computing in
Taiwan, • PRAGMA 15, Fall 2008 will be hosted by the Universiti Sains Malaysia in Malaysia.
CAMPUS GRID WORKSHOP , ICT RESEARCH PLATFORM, 16 MAY 2007
PRAGMA’s gathering old & new….• PRAGMA 1 March, 2002 at the San Diego Supercomputer Center at the University
of California at San Diego. • PRAGMA 2 Seoul, Korea, Korea Institute of Science and Technology Information
(KISTI). • PRAGMA 3, Fukuoka, Japan - January 2003, AIST & Osaka U• PRAGMA 4, Melbourne, Australia, June 2003, APAC • PRAGMA 5 , Taipei, Taiwan, October 2003, NCHC • PRAGMA 6, Beijing, China, May, 2004, Chinese Academy of Science (CNIC) • PRAGMA 7, SDSC, September 15-17, 2004 (SDSC)• PRAGMA 8, Singapore, May 2005, BII and National Grid Office (Singapore). • PRAGMA 9, Hyderabad, October 2005, University of Hyderabad in Hyderabad,
India. • PRAGMA 10, Townsville, Queensland, Australia in March 2006, APAC, Monash U• PRAGMA 11 Osaka, Japan October 15-18, 2006, Osaka U.• PRAGMA 12 Bangkok, Thailand, March 20-22, 2007, Kasertsart U, Thai Grid Office.• PRAGMA 13 Urbana-Champaign, IL (USA), September 23-25, 2007, NCSA.• PRAGMA 14, Spring 2008, National Center for High-performance Computing in
Taiwan, • PRAGMA 15, Fall 2008 will be hosted by the Universiti Sains Malaysia in Malaysia.
CAMPUS GRID WORKSHOP , ICT RESEARCH PLATFORM, 16 MAY 2007
PRAGMA’s gathering old & new….• PRAGMA 1 March, 2002 at the San Diego Supercomputer Center at the University
of California at San Diego. • PRAGMA 2 Seoul, Korea, Korea Institute of Science and Technology Information
(KISTI). • PRAGMA 3, Fukuoka, Japan - January 2003, AIST & Osaka U• PRAGMA 4, Melbourne, Australia, June 2003, APAC • PRAGMA 5 , Taipei, Taiwan, October 2003, NCHC • PRAGMA 6, Beijing, China, May, 2004, Chinese Academy of Science (CNIC) • PRAGMA 7, SDSC, September 15-17, 2004 (SDSC)• PRAGMA 8, Singapore, May 2005, BII and National Grid Office (Singapore). • PRAGMA 9, Hyderabad, October 2005, University of Hyderabad in Hyderabad,
India. • PRAGMA 10, Townsville, Queensland, Australia in March 2006, APAC, Monash U• PRAGMA 11 Osaka, Japan October 15-18, 2006, Osaka U.• PRAGMA 12 Bangkok, Thailand, March 20-22, 2007, Kasertsart U, Thai Grid Office.• PRAGMA 13 Urbana-Champaign, IL (USA), September 23-25, 2007, NCSA.• PRAGMA 14, Spring 2008, National Center for High-performance Computing in
Taiwan, • PRAGMA 15, Fall 2008 will be hosted by the Universiti Sains Malaysia in Malaysia.
80% Attendence !
CAMPUS GRID WORKSHOP , ICT RESEARCH PLATFORM, 16 MAY 2007
12/15 Workshop: Reaping benefits from PRAGMA’s
• Excellent networking • Impact on the career:
– Steering Committee, JSPS Fellowship (under Nakamura-sensei), PRIUS Lectures, Travel Grants (Osaka U)
• Impact on research– NADI/NAPIMM; NADI-VISAGE (with Osaka U,
PRIUS Students)– Avian Flu Grid; Avian Flu’s Group * Grant– Focus on Infectious Diseases– Establish Research Facilities
CAMPUS GRID WORKSHOP , ICT RESEARCH PLATFORM, 16 MAY 2007
My View of PRAGMA benefitting Community
• SARS: Grid Community Pulls together to Battle SARS
• GLEON: Launching a new community effort– Building on EcoGrid in Taiwan
• Expanding Reach of Projects– Optiputer; NEESit; iGEON; IVOA
• PRIME & PRIUS: Creating opportunities for undergraduate students
CAMPUS GRID WORKSHOP , ICT RESEARCH PLATFORM, 16 MAY 2007
Grid Computing & Pharmaceutical Sciences
NADI-VISAGENatural Drug Discovery Intelligence-
Virtual Screening Application in Grid EnvironmentMitsuru Jikeya, Masafumi Tominaga, Suhaini Ahmad, Susumu Date,
Shinji Shimojo, Toru Fujimara and Habibah A Wahab
CAMPUS GRID WORKSHOP , ICT RESEARCH PLATFORM, 16 MAY 2007
INTRODUCING NAPIMm©
• COMPUTATIONAL PLATFORM– Grid enabled molecular modelling platform– Automatic docking & reverse docking server– MD simulation server– Protein-structure prediction server
• DATABASE SYSTEM: NADI©
– NADI-CHEM©
– MNATCHEM©
– NADI-RA©
– NADI-HERBS©
CAMPUS GRID WORKSHOP , ICT RESEARCH PLATFORM, 16 MAY 2007
NaDI©: Features
• COPYRIGHTED DATABASE SYSTEM• Comprehensive 3D chemical structure Database
of natural products– Inclusive of chemical properties and biological activities
references– 2D structures– 3D structures ready for in silico drug screening
• Drug Receptor Database – – provide drug receptor and disease information.– 3D structure of drug target
• Herbal Monographs– Comprehensive description about traditional uses of
Malaysian medicinal plants
CAMPUS GRID WORKSHOP , ICT RESEARCH PLATFORM, 16 MAY 2007
CAMPUS GRID WORKSHOP , ICT RESEARCH PLATFORM, 16 MAY 2007
NatPro 2005 BioMalaysia 2005
Campus Grid Launching 2005 ITEX 2005
CAMPUS GRID WORKSHOP , ICT RESEARCH PLATFORM, 16 MAY 2007
CAMPUS GRID WORKSHOP , ICT RESEARCH PLATFORM, 16 MAY 2007
MeOH
BuOH
EtOAc
n-hexane
Concentrate in vacuo to 10% of total extract
Dried plants, powdered
Soxhlet extraction
Active extracts
n-hexane fractions
aqueous
EtOAcfractions
aqueous
BuOHfractions
aqueousfractions
All fractions will be further fractionated using column chromatographic methodsIsolation and purifications using TLC, Prep-LC methods
Pure compounds
Structural elucidation using spectral analyses(UV, IR, NMR, MS)
HPLC/LCMS profilings Screening for anti-influenza activity
Storage and catalogue all the compounds obtained
Purchased compounds
CAMPUS GRID WORKSHOP , ICT RESEARCH PLATFORM, 16 MAY 2007
NADI’s Applications
• Dengue: Screen 250 flavonoids, confirm panduratin as most promising agent
• TB: • Avian Flu : On-going work on 4000
Malaysian’s nature chemicals
Sialic acids & Sialidase inhibitors
CAMPUS GRID WORKSHOP , ICT RESEARCH PLATFORM, 16 MAY 2007
CAMPUS GRID WORKSHOP , ICT RESEARCH PLATFORM, 16 MAY 2007
Thank You