Biosciences Working Group Update

Wilfred W. Li, Ph.D., UCSD, USA

Habibah Wahab, Ph.D., USM, Malaysia

You-Qiang Song, Ph.D, HKU, PRC

Hosted by HKUHong Kong, PRC, March 2-4, 2010

PRAGMA: model for international collaboration in Technology and Science

Broadening Impact of TechnologyEngaging Future Generations

PRIME Student 2009: Jessica Hsieh, USM

Scientific Drivers and Use Cases: Influenza A Virus

http://www.reactome.org/http://www.wikipedia.org http://library.thinkquest.org/05aug/01479/prevention1.html

Harris et al, PNAS, 2006

2009 H1N1 Pandemic Influenza

Source: http://flutracker.rhizalabs.com/

•Cumulative cases represented in Google Map as of 21 Apr, 2010•WHO: 18769 deaths to date•US: 4642 deaths; 480230 total cases•Malaysia: 74 deaths, 6463 total cases•China: 650 deaths; 124300 total cases

•Postpandemic period as of Aug 2010•0.5~1% death rate, similar to seasonal flu•Targets younger and healthy individuals, different from seasonal flu (90% > 65 years older)

WHO Status UpdateWeek 17 (Apr 19, 2009) to Week 13 (Apr 3, 2010)

http://www.who.int/csr/disease/swineflu/laboratory23_04_2010/en/index.html

Transparent access of applications on Avian Flu Grid through middleware

CNIC Duckling Portal

Konkuk/KukminGlyco-M*Grid

NBCR CADD

Relaxed Complex Scheme and Ensemble based Virtual Screening Contributed to HIV Integrase Inhibitor Development

“ Exploration of the structural basis for this unexpected result … suggests an approach to the development of integrase inhibitors with unique resistance profiles.”

D. Hazuda et al., Proc. Natl. Acad. Sci. USA (Aug. 2004), refers to Schames, et al. (2004).

Discovery of unexpected binding site in HIV-1 Integrase using MD and AutoDock: Schames, … & McCammon, J. Med. Chem. (released on web, early 2004)

February, 2006 – Phase III Clinical TrialsFebruary, 2007 – Name announced: Isentress (raltegravir)October, 2007 – FDA “fast track” approval

New Class of HIV Drugs: Merck & Co.

MK-0518

Source: A. McCammon

Ensemble-based Virtual Screening with Relaxed Complex SchemeNAMD2Amber

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.

Source: Amaro

Advances in Computing Infrastructure Enables Complex Simulations of Biomolecular Systems

Amaro & Li, CTMC, 2010

Opal 2 for SaaS

Condor pool TeraGrid/PRAGMA Grid PBS/SGE Clusters

Globus

Opal Application Services

Opal App MGLTools KeplerOpal WS: Transparent Access Layer for Applications

Grid/Cloud ResourcesGrid/Cloud Resources

CADD VistrailsTaverna

Condor CSF4

Opal Plugins for Popular Workflow Software

14

CADD: Opal Web Services for Biomedical Applications

• Ren et al, NAR 2010, Web Server Issue

• http://cadd.nbcr.net

• Modules supporting MD simulation and analysis, Virtual Screening, Docking, Visualization

• Project management under development

Opal MetaService: Transparent Access to Workflows and Applications

Social Networks and Collaborative Environment

Are these too big to fail?Utility Computing finally?

• OPAL as resource manager of CSF4• CSF4 allocate service instances of OPAL for jobs

1717

New OPAL-CSF4 Cloud model

PRAGMA 19 workshop, Changchun, Jilin, China, Sep.13-15, 2010.

2 – 4 March 2010 PRAGMA 18, San Diego 18

Integrating Visualization Workflows using Real-time bioMEdical data Streaming and visualization (RIMES)

Kevin Dong, CNIC

Biomedical CLOUD

Resource Manager(edu.sdsc.nbcr.opal.manager.CSFJobManager)

Service Manager

Scheduling: Workflow Job

Array Job

AutoDock NAMD

OPAL2

CSF4

User Interface

Grid Sites

MetaScheduler

generate RSL files

Grid Resources

Input/Ouput Files: StageIn and StageOut

VM Replication Experimenthttp://goc.pragma-grid.net/wiki/index.php/VC-replication-2

SDSC VM hosting server AIST VM hosting server

AFG VM(original) AFG VM

(copy)

• VM hosting server: •Rocks 5.3 Xen roll

• Avian Flu Grid VM• Rocks VM• Globus/SGE• Autodock

• Replication updates • hostname and IP • Compute nodes• Network configurations• Globus configuration• SGE configuration

NBCR VM hosting server

AFG VM(copy)

VM replication

Lau, Haga and Date

ViewDock TDW

Other Examples of Continued Software Development at Member Institutions

– Drugscreener-G – KISTI, Korea– Grid Enabled Virtural Screening Service – ASGC,

Taiwan– CADD Pipeline – NBCR, USA– WISDOM project – CNRS, EU– Glyco-M*Grid – Kookmin & Konkuk U, Korea

Meeting the New Challenges

• Virtualization – What does it mean to us?– Virtual machines, CSF server, Gfarm server and virtual

clusters

• Production environment – Where is it? What form should it take? -- EC2, VC replication

• Collaboration – How to stay in touch better, PRIME, MURPA, research in general?

Look Around Session

• Heru Suhartanto – Indonesia Faculty of Computer Science, University of

Indonesia – Molecular Dynamics Simulation of disordered

regions the RGK-family of small GTPase revealed no GTPase activity

• Suntae Hwang – South Korea Kookmin University – MGrid Service on Nationwide Consortium of

Supercomputing Infrastructure (PLSI) in Korea

PRAGMA 19:Look ahead sessionsProgress Reported at PRAGMA 20!

• Day 2-– Duckling portal as a new generation user portal

• Current focus: better user management, online editing, status notification

• Possible features: – Support for Opal service? Compute cloud access?– Support for larger data size? Or Data cloud access?– Support for Open ID? Social network access?– Continued support for RIMES?

Looking ahead

– M*Grid portal• Current status: pending deployment in PLSI e-science

project, with Gfarm filesystem browser• Possible features:

– Duckling portal as the new portlet framework?– Possible metascheduler in resource selection?– Possible Opal service support? M*Grid job execution

environment is quite feature rich, and specific for simulation jobs. Can Opal service support provide more benefits?

Looking ahead

• CSF4– Current focus: CSF4 support for Opal services

(maybe globus no longer needed for job execution), cloud service metascheduler, bug fixes and release of 4.0.6

• Possible features: more efficient/advanced resource selection policies

• Gfarm– Current focus: Gfarm 2.4 deployment and

integration with Opal 2.3

Looking ahead

• NBCR CADD– Current focus: Release of 0.1 beta,

documentation, and RCS rescoring workflow– Possible features:

• Data cloud service• Metadata and job history