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Biosciences Working Group Update & Report Back

Biosciences Working Group Update & Report Back. Wilfred W. Li, Ph.D., UCSD, USA Habibah Wahab, Ph.D., USM, Malaysia Hosted by IOIT Hanoi, Vietnam, Oct 29, 2009. Recap of PRAGMA 16 – Daejon, Korea, Mar 2009. Infectious Diseases Research in Cyberinfrastructure (iDRiC Workshop)--KISTI

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Biosciences Working Group Update & Report Back

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  1. Biosciences Working Group Update& Report Back Wilfred W. Li, Ph.D., UCSD, USA Habibah Wahab, Ph.D., USM, Malaysia Hosted by IOIT Hanoi, Vietnam, Oct 29, 2009

  2. Recap of PRAGMA 16 – Daejon, Korea, Mar 2009 • Infectious Diseases Research in Cyberinfrastructure (iDRiC Workshop)--KISTI • Drugscreener-G – KISTI, Korea • Grid Enabled Virtural Screening Service – ASGC, Taiwan • CADD Pipeline – NBCR, USA • WISDOM project – CNRS, EU • Glyco-M*Grid – Kookmin & Konkuk U, Korea

  3. Follow-up activities • Continued development of application specific services – AutoDock, NAMD as Opal services • Continued development of workflows – NBCR Summer Institute training of CADD pipeline • Glyco-M*Grid – Suntae Hwang • Release of Opal 2.1 with condor and CSF4 4.0.5.1 plugins • Ability to use Condor web service interface for virtual screening using TeraGrid

  4. New Since PRAGMA 16 • Real-time bioMEdical data Streaming and visualization (RIMES) – CNIC, China • PRIME Students • USM, NTU, CNIC • Osaka U., Monash U. • New in 2010: JLU, host of PRAGMA 19 • MURPA Students • Cheminformatics and Nimrod/K based workflows • Calit2 Summer Internship • Kevin Wu

  5. Real-time bioMEdical data Streaming and visualization (RIMES) Kevin Dong, CNIC

  6. Next Milestone • Production use of Gfarm for sharing simulation data • Production use by PRAGMA 18 • Virtual machine scheduling using CSF4 • Demonstration by PRAGMA 19

  7. Scientific Results Newhouse et al, JACS 2009

  8. PRIME/Calit2 Summer Project

  9. New Challenges • Virtualization – What does it mean to us? • Production environment – Where is it? What form should it take? • The Connection between Productivity and Grid/Cloud – Most work is still done on local clusters, the desire to use the grid/Cloud is there, but the infrastructure is still evolving • Sociology of software engineering – Can we collaborate using Facebook?

  10. GAP -- The architecture overview Common Interface to Heterogeneous Environment Service Oriented Architecture Multi-user Environment Portable & light-weight Client H-Y. Chen, ASGC

  11. http://demo.mgrid.or.kr http://service.mgrid.or.kr S Huang, KU Parallel Processing Lab.

  12. Concluding Remark • Please visit the demo site http://demo.mgrid.or.kr • and use the site http://service.mgrid.or.kr Parallel Processing Lab.

  13. Themes • Technology trend and user service • Shared development • Diversity and outreach, other biological problems and associated challenges • CDI library for virtual screening • Public ones free for use • GVS – based upon Glite

  14. 4) Training and education opportunities • ISGC annual meeting, one day or two day workshop • Diana, Ganga • Sharing of experience • Make user participate default VO with resources • Users may want to use different programs, rescoring, associated support

  15. Application Deployment • Jopera • Different workflows. Conversion is difficult between workflow programs • GEMLCA – Globus related development • M*Grid • Looking for users • Setting up PRAGMA instance • How to use Gfarm

  16. Application Sharing and Testing • RIMES • Kookmin will test RIMES • Authentication mechanism • How can we use the Tsukuba-GAMA authentication?

  17. Lessons on the Grid • CNGrid • Education network • ChinaGrid • BioinformationGrid – Qinghua University

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