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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. AI 2008, Bangkok, Thailand Jan 22-25, 2008 4 year Anniversary of 1 st AI outbreak.

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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
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.



Avian flu grid one year later @ pragma 14
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


Transparent access of applications on avian flu grid through middleware
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 middleware

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.




Host tropism studies for avian influenza and human adaptation
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



Glyco mgrid and vs mgrid
Glyco-Mgrid adaptation and VS-Mgrid

YoungjinChoi, Karpjoo Jeong


Enabling biomedical applications with grid technology cyberinfrastructure
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


Opal web service toolkit

Web Portals Cyberinfrastructure

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


Opal csf4 integration

C Cyberinfrastructure

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Opal CSF4 Integration


Usage scenario
Usage Scenario Cyberinfrastructure

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


Pdb2pqr advanced submission form
PDB2PQR Advanced Submission Form Cyberinfrastructure

Exclusive group

Input file

Group 1

String

Group 2

Exclusive enumeration

Group 3

Flag

Group 4



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