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CAMPUS GRID WORKSHOP, ICT RESEARCH PLATFORM, 16 MAY 2007 PRAGMA : My personal hope & future Habibah A Wahab, School of Pharmaceutical Sciences, Universiti.

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Presentation on theme: "CAMPUS GRID WORKSHOP, ICT RESEARCH PLATFORM, 16 MAY 2007 PRAGMA : My personal hope & future Habibah A Wahab, School of Pharmaceutical Sciences, Universiti."— Presentation transcript:

1 CAMPUS GRID WORKSHOP, ICT RESEARCH PLATFORM, 16 MAY 2007 PRAGMA : My personal hope & future Habibah A Wahab, School of Pharmaceutical Sciences, Universiti Sains Malaysia

2 CAMPUS GRID WORKSHOP, ICT RESEARCH PLATFORM, 16 MAY 2007 PRAGMA: INVOLVEMENT BY CHANCE 2001 –27 th Aug: Presenting TB work in American Chemical Society Meeting –28 th Aug: Invited to present seminar in Institute for TB Research, Univ. Illinois in Chicago –29 th 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 –Jan: P. Arzberger invited USM to join the Inaugral PRAGMA meeting. –Chan Huah Yong to present Grid Research Group –Habibah to attend as observer.

3 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.

4 CAMPUS GRID WORKSHOP, ICT RESEARCH PLATFORM, 16 MAY 2007 PRAGMAs MISSION Among a community of investigators in the Pacific Rim – Establish sustained collaborations – Advance the use of the grid technologies in scientific applications

5 CAMPUS GRID WORKSHOP, ICT RESEARCH PLATFORM, 16 MAY 2007 USM & PRAGMA Commitment to PRAGMAs Mission –Sharing of resources: USM contributes a total of 34 nodes (51 cpus) to PRAGMAs test-bed. –Host PRAGMAs meeting – All are welcome to PRAGMA th October, 2008 in USMs main campus, Penang, Malaysia. –Real Grid Applications: AutoDock on the Grid, AMEXg, AMBER in Gfarm –Participate in PRIUSs 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)

6 CAMPUS GRID WORKSHOP, ICT RESEARCH PLATFORM, 16 MAY 2007

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9 BIOSCIENCE

10 CAMPUS GRID WORKSHOP, ICT RESEARCH PLATFORM, 16 MAY 2007

11 PRAGMA Grid Testbed AIST, Japan CNIC, China KISTI, Korea ASCC, Taiwan NCHC, Taiwan UoHyd, India MU, Australia BII, Singapore KU, Thailand USM, Malaysia NCSA, USA SDSC, USA CICESE, Mexico UNAM, Mexico UChile, Chile TITECH, Japan

12 CAMPUS GRID WORKSHOP, ICT RESEARCH PLATFORM, 16 MAY 2007 PRAGMA Grid Resources

13 CAMPUS GRID WORKSHOP, ICT RESEARCH PLATFORM, 16 MAY 2007 PRAGMAs 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.

14 CAMPUS GRID WORKSHOP, ICT RESEARCH PLATFORM, 16 MAY 2007 PRAGMAs 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.

15 CAMPUS GRID WORKSHOP, ICT RESEARCH PLATFORM, 16 MAY 2007 PRAGMAs 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 !

16 CAMPUS GRID WORKSHOP, ICT RESEARCH PLATFORM, 16 MAY /15 Workshop: Reaping benefits from PRAGMAs 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 Flus Group * Grant –Focus on Infectious Diseases –Establish Research Facilities

17 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

18 CAMPUS GRID WORKSHOP, ICT RESEARCH PLATFORM, 16 MAY 2007 Grid Computing & Pharmaceutical Sciences NADI-VISAGE Natural Drug Discovery Intelligence- Virtual Screening Application in Grid Environment Mitsuru Jikeya, Masafumi Tominaga, Suhaini Ahmad, Susumu Date, Shinji Shimojo, Toru Fujimara and Habibah A Wahab

19 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 ©

20 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

21 CAMPUS GRID WORKSHOP, ICT RESEARCH PLATFORM, 16 MAY 2007

22 NatPro 2005BioMalaysia 2005 Campus Grid Launching 2005ITEX 2005

23 CAMPUS GRID WORKSHOP, ICT RESEARCH PLATFORM, 16 MAY 2007

24 MeOH BuOH EtOAc n-hexane Concentrate in vacuo to 10% of total extract Dried plants, powdered Soxhlet extraction Active extracts n-hexane fractions aqueous EtOAc fractions aqueous BuOH fractions aqueous fractions All fractions will be further fractionated using column chromatographic methods Isolation and purifications using TLC, Prep-LC methods Pure compounds Structural elucidation using spectral analyses (UV, IR, NMR, MS) HPLC/LCMS profilingsScreening for anti-influenza activity Storage and catalogue all the compounds obtained Purchased compounds Flow Chart of the Research Activities

25 CAMPUS GRID WORKSHOP, ICT RESEARCH PLATFORM, 16 MAY 2007 NADIs Applications Dengue: Screen 250 flavonoids, confirm panduratin as most promising agent TB: Avian Flu : On-going work on 4000 Malaysians nature chemicals

26 Sialic acids & Sialidase inhibitors

27 CAMPUS GRID WORKSHOP, ICT RESEARCH PLATFORM, 16 MAY 2007

28 Thank You


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