biosciences working group update wilfred w. li, ph.d., ucsd karpjoo jeong, ph.d., konkuk university,...
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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
H5N1 Pandemic Threat
source: Bankok Post; Normile, D. Science, 319:1178-9.
AI 2008, Bangkok, ThailandJan 22-25,20084 year Anniversaryof 1st AI outbreak
Points of Intervention in Viral Infectious Cycle
De Clercq, Nat Rev, 2006
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
Transparent access of applications on Avian Flu Grid through middleware
Gfarm File System
applications
databases
/gfs/$USER
NAMDAutoDock
Zinc NCIDS
Virtual Directory Tree
H5N1 related glycan conformation analysis
using M*Grid and Glyco-M*Grid
Relaxed Complex Method Molecular
Dynamics Simulation Data Sets & Database
Virtual Screening Data Sets & Database
PRAGMA PortalMy WorkSphere
CSF4 Server
HPC Clusters, NBCR,
TeraGrid, MHPCC
Mr. Bayes
Opal poster, PRAGMA 13
AFG poster, PRAGMA 13
Ensemble-based Virtual Screening with Relaxed Complex Scheme
NAMD2Amber
NCI Diversity Set: 3.3 MB, 2000 compounds;Required at each siteZINC subset: 200,000. A few hundred MB
Multiple targets: HA, NA subtypesEach 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 interactionWith 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 Organizations Web Service
KEPLER
Workflow Management
Vision Virtual Filesystem
Security Services (GAMA)
Opal Web Service Toolkit
Condor pool SGE Cluster PBS Cluster
Globus DRMAA Globus
Application Services
StateMgmt
Web Portals MGL Tools KeplerContinuity
http://nbcr.net/software/opal
Opal CSF4 Integration Cluster
Cluster
Cluster
App X
App Y Other Resource
12 CPUs
App X
App Z
Other Resource
64 CPUs
App Y
App Z 8 CPUs
Other Resource
CSF4 M eta-Scheduler
Resource Status List
MDS
Resource
Scheduling Modules
Resource Requirements
App X10 CPUs
App Z40 CPUs
App X5 CPUs
App Y1 CPU
Tomcat Container
Axis Engine
Opal WS Opal WS
getAppMetadata
launchJob
getOutput
…
PDB2PQR
getAppMetadata
launchJob
getOutput
…
MEME
…Opal server
Opal GUI
displayForm PDB2PQR
getAppMetadata
appMetadata
submissionFormUser
On user submit:• Invoke launchJob with right input
parameters
Usage Scenario1
5
4
32
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