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

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Presentation on theme: "Biosciences Working Group Update Wilfred W. Li, Ph.D., UCSD Karpjoo Jeong, Ph.D., Konkuk University, South Korea Habibah Wahab, Ph.D., USM, Malaysia."— Presentation transcript:

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

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

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

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 NAMD2 Amber NCI Diversity Set: 3.3 MB, 2000 compounds; Required at each site ZINC subset: 200,000. A few hundred MB Multiple targets: HA, NA subtypes Each target: 30~50 MD snapshots, 1~2 MB each AutoDock4 Simulation Data: hundreds of GB Docking Data: hundreds of MB 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 Q224L and G226S mutations at HA receptor binding domain (RBD) in H5 are implicated in host specificity switch Indonesia Karo Strain of H5N1 interaction With avian receptor analogue LSTa Q224L and G226S mutations modeled Into Karo strain Host tropism studies for Avian Influenza and human adaptation

10 CNIC: Guangyuan Liu, Kai Nan

11 Glyco-Mgrid and VS-Mgrid Youngjin Choi, Karpjoo Jeong

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

13 Security Services (GAMA) Opal Web Service Toolkit Condor poolSGE Cluster PBS Cluster GlobusDRMAAGlobus Application Services State Mgmt Web PortalsMGL ToolsKeplerContinuity http://nbcr.net/software/opal

14 Opal CSF4 Integration

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

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

17 Vision Based Grid Workflow Environment

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