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Biosciences Working Group Update

Biosciences Working Group Update. Wilfred W. Li, Ph.D., UCSD Karpjoo Jeong, Ph.D., Konkuk University, South Korea Habibah Wahab, Ph.D., USM, Malaysia. H5N1 Pandemic Threat. AI 2008, Bangkok, Thailand Jan 22-25, 2008 4 year Anniversary of 1 st AI outbreak.

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Biosciences Working Group Update

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  1. Biosciences Working Group Update Wilfred W. Li, Ph.D., UCSD Karpjoo Jeong, Ph.D., Konkuk University, South Korea Habibah Wahab, Ph.D., USM, Malaysia

  2. H5N1 Pandemic Threat AI 2008, Bangkok, Thailand Jan 22-25, 2008 4 year Anniversary of 1st AI outbreak source: Bankok Post; Normile, D. Science, 319:1178-9.

  3. Points of Intervention in Viral Infectious Cycle De Clercq, Nat Rev, 2006

  4. Avian Flu Grid: one year later @ PRAGMA 14 Avian Flu Grid @ AFG workshop, HI, USA, August 2007 Avian Flu Grid Project @ PRAGMA 12, Bangkok, Thailand, March 2007 Funded by TATRC, NSF, and PRAGMA member institutes

  5. Transparent access of applications on Avian Flu Grid through middleware Opal poster, PRAGMA 13 AFG poster, PRAGMA 13

  6. 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.

  7. Oseltamivir (Tamiflu) bound to Neuraminidase Catalytic Cavity

  8. NA active site domain is intrinsically flexible and offers new drug design opportunities

  9. Host tropism studies for Avian Influenza and human adaptation Indonesia Karo Strain of H5N1 interaction With avian receptor analogue LSTa Q224L and G226S mutations modeled Into Karo strain Q224L and G226S mutations at HA receptor binding domain (RBD) in H5 are implicated in host specificity switch

  10. CNIC: Guangyuan Liu, Kai Nan

  11. Glyco-Mgrid and VS-Mgrid YoungjinChoi, Karpjoo Jeong

  12. Enabling Biomedical Applications with Grid Technology -- Cyberinfrastructure Cyberinfrastructure: raw resources, middleware and execution environment Virtual Organizations Workflow Management Web Service NBCR Rocks Clusters Vision Virtual Filesystem KEPLER

  13. Web Portals Continuity MGL Tools Kepler Opal Web Service Toolkit State Mgmt Security Services (GAMA) Application Services Globus DRMAA Globus PBS Cluster Condor pool SGE Cluster http://nbcr.net/software/opal

  14. C l u s t e r A p p X Tomcat Container A p p X 1 2 C P U s 5 C P U s O t h e r A p p Y R e s o u r c e A p p X Axis Engine 1 0 C P U s C l u s t e r A p p Z 4 0 C P U s Opal WS Opal WS C S F 4 M e t a - S c h e d u l e r A p p X 6 4 C P U s O t h e r A p p Y R e s o u r c e S c h e d u l i n g M o d u l e s A p p Z A p p Y R e s o u r c e S t a t u s L i s t 1 C P U C l u s t e r M D S A p p Z 8 C P U s O t h e r R e s o u r c e R e s o u R e s o u r c e r c e R e q u i r e m e n t s Opal CSF4 Integration

  15. Usage Scenario On user submit: Invoke launchJob with right input parameters Opal GUI User getAppMetadata getAppMetadata MEME PDB2PQR launchJob launchJob getOutput getOutput … … 1 displayForm PDB2PQR 4 submissionForm 5 3 appMetadata 2 getAppMetadata … Opal server

  16. PDB2PQR Advanced Submission Form Exclusive group Input file Group 1 String Group 2 Exclusive enumeration Group 3 Flag Group 4

  17. Vision Based Grid Workflow Environment

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