campus grid workshop, ict research platform, 16 may 2007 pragma : my personal hope & future...

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


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.


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.


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


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)


BIOSCIENCE


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


PRAGMA Grid Resources

http://pragma-goc.rocksclusters.org/pragma-doc/resources.html


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.


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 !


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


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


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


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©


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


NatPro 2005 BioMalaysia 2005

Campus Grid Launching 2005 ITEX 2005


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


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


Thank You

campus grid workshop, ict research platform, 16 may 2007 pragma : my personal hope & future...

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