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Biosciences Working Group Update

Biosciences Working Group Update. Wilfred W. Li, Ph.D., UCSD, USA Habibah Wahab, Ph.D., USM, Malaysia You-Qiang Song, Ph.D, HKU, PRC Hosted by HKU Hong Kong, PRC, March 2-4, 2010. PRAGMA: model for international collaboration in Technology and Science.

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Biosciences Working Group Update

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  1. Biosciences Working Group Update Wilfred W. Li, Ph.D., UCSD, USA Habibah Wahab, Ph.D., USM, Malaysia You-Qiang Song, Ph.D, HKU, PRC Hosted by HKU Hong Kong, PRC, March 2-4, 2010

  2. PRAGMA: model for international collaboration in Technology and Science

  3. Broadening Impact of TechnologyEngaging Future Generations PRIME Student 2009: Jessica Hsieh, USM

  4. Scientific Drivers and Use Cases: Influenza A Virus Harris et al, PNAS, 2006 http://www.reactome.org/ http://www.wikipedia.org http://library.thinkquest.org/05aug/01479/prevention1.html

  5. 2009 H1N1 Pandemic Influenza • Cumulative cases represented in Google Map as of 21 Apr, 2010 • WHO: 18769 deaths to date • US: 4642 deaths; 480230 total cases • Malaysia: 74 deaths, 6463 total cases • China: 650 deaths; 124300 total cases • Postpandemic period as of Aug 2010 • 0.5~1% death rate, similar to seasonal flu • Targets younger and healthy individuals, different from seasonal flu (90% > 65 years older) Source: http://flutracker.rhizalabs.com/

  6. WHO Status Update Week 17 (Apr 19, 2009) to Week 13 (Apr 3, 2010) http://www.who.int/csr/disease/swineflu/laboratory23_04_2010/en/index.html

  7. Transparent access of applications on Avian Flu Grid through middleware CNIC Duckling Portal Konkuk/KukminGlyco-M*Grid NBCR CADD

  8. Relaxed Complex Scheme and Ensemble based Virtual Screening Contributed to HIV Integrase Inhibitor Development Discovery of unexpected binding site in HIV-1 Integrase using MD and AutoDock:Schames, … & McCammon, J. Med. Chem. (released on web, early 2004) MK-0518 “Exploration of the structural basis for this unexpected result … suggests an approach to the development of integrase inhibitors with unique resistance profiles.” D. Hazuda et al., Proc. Natl. Acad. Sci. USA (Aug. 2004), refers to Schames, et al. (2004). February, 2006 – Phase III Clinical Trials February, 2007 – Name announced: Isentress (raltegravir) October, 2007 – FDA “fast track” approval New Class of HIV Drugs: Merck & Co. Source: A. McCammon

  9. Ensemble-based Virtual Screening with Relaxed Complex Scheme NCI Diversity Set: 3.3 MB, 2000 compounds; Required at each site ZINC subset: 200,000. A few hundred MB NAMD2 Amber AutoDock4 Docking Data: hundreds of MB Multiple targets: HA, NA subtypes Each target: 30~50 MD snapshots, 1~2 MB each Simulation Data: hundreds of GB Total data to date: ~5 TB in long term storage. Each experiment is about 1 Petaflops accumulative in computation cost. Source: Amaro

  10. Advances in Computing Infrastructure Enables Complex Simulations of Biomolecular Systems Amaro & Li, CTMC, 2010

  11. Opal 2 for SaaS

  12. Opal WS: Transparent Access Layer for Applications Opal App MGLTools CADD Taverna Vistrails Kepler Opal Application Services Grid/Cloud Resources Condor CSF4 Globus PBS/SGE Clusters Condor pool TeraGrid/PRAGMA Grid

  13. Opal Plugins for Popular Workflow Software

  14. CADD: Opal Web Services for Biomedical Applications • Ren et al, NAR 2010, Web Server Issue • http://cadd.nbcr.net • Modules supporting MD simulation and analysis, Virtual Screening, Docking, Visualization • Project management under development

  15. Opal MetaService: Transparent Access to Workflows and Applications

  16. Social Networks and Collaborative Environment Are these too big to fail? Utility Computing finally?

  17. New OPAL-CSF4 Cloud model • OPAL as resource manager of CSF4 • CSF4 allocate service instances of OPAL for jobs 17 PRAGMA 19 workshop, Changchun, Jilin, China, Sep.13-15, 2010.

  18. PRAGMA 18, San Diego Nornisah Mohamed, USM

  19. Integrating Visualization Workflows using Real-time bioMEdical data Streaming and visualization (RIMES) Kevin Dong, CNIC

  20. VM Replication Experimenthttp://goc.pragma-grid.net/wiki/index.php/VC-replication-2 • VM hosting server: • Rocks 5.3 Xen roll • Avian Flu Grid VM • Rocks VM • Globus/SGE • Autodock • Replication updates • hostname and IP • Compute nodes • Network configurations • Globus configuration • SGE configuration AFG VM (original) VM replication AFG VM (copy) AFG VM (copy) SDSC VM hosting server AIST VM hosting server NBCR VM hosting server

  21. ViewDock TDW Lau, Haga and Date

  22. Other Examples of Continued Software Development at Member Institutions • 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

  23. Meeting the New Challenges • Virtualization – What does it mean to us? • Virtual machines, CSF server, Gfarm server and virtual clusters • Production environment – Where is it? What form should it take? -- EC2, VC replication • Collaboration – How to stay in touch better, PRIME, MURPA, research in general?

  24. Look Around Session • Heru Suhartanto • Indonesia Faculty of Computer Science, University of Indonesia • Molecular Dynamics Simulation of disordered regions the RGK-family of small GTPase revealed no GTPase activity • Suntae Hwang • South Korea Kookmin University • MGrid Service on Nationwide Consortium of Supercomputing Infrastructure (PLSI) in Korea

  25. PRAGMA 19:Look ahead sessionsProgress Reported at PRAGMA 20! • Day 2- • Duckling portal as a new generation user portal • Current focus: better user management, online editing, status notification • Possible features: • Support for Opal service? Compute cloud access? • Support for larger data size? Or Data cloud access? • Support for Open ID? Social network access? • Continued support for RIMES?

  26. Looking ahead • M*Grid portal • Current status: pending deployment in PLSI e-science project, with Gfarm filesystem browser • Possible features: • Duckling portal as the new portlet framework? • Possible metascheduler in resource selection? • Possible Opal service support? M*Grid job execution environment is quite feature rich, and specific for simulation jobs. Can Opal service support provide more benefits?

  27. Looking ahead • CSF4 • Current focus: CSF4 support for Opal services (maybe globus no longer needed for job execution), cloud service metascheduler, bug fixes and release of 4.0.6 • Possible features: more efficient/advanced resource selection policies • Gfarm • Current focus: Gfarm 2.4 deployment and integration with Opal 2.3

  28. Looking ahead • NBCR CADD • Current focus: Release of 0.1 beta, documentation, and RCS rescoring workflow • Possible features: • Data cloud service • Metadata and job history

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