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 transcript:

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

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

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

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

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.

Oseltamivir (Tamiflu) bound to Neuraminidase Catalytic Cavity

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

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

CNIC: Guangyuan Liu, Kai Nan

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

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

Security Services (GAMA) Opal Web Service Toolkit Condor poolSGE Cluster PBS Cluster GlobusDRMAAGlobus Application Services State Mgmt Web PortalsMGL ToolsKeplerContinuity

Opal CSF4 Integration

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

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

Vision Based Grid Workflow Environment