PRAGMA Institute on Implementation @ PRAGMA 19

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

Xiaohui Wei, Ph.D., JLU, PRC

Hosted by JLUChangchun, Jilin, PRC, Sept 13, 2010

Avian Flu Grid: Transition from Grid to Cloud Computing

Scientific Driver and Use Cases

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

Harris et al, PNAS, 2006

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

New Challenges

• Virtualization – What does it mean to us?– Rock’n Rolls, on demand virtual machines,

• Production environment – Where is it? What form should it take?– GPU clusters, virtual machines, cloud services

• Most work is still done on local clusters, the desire to use the grid/Cloud is there– It’s happening, and quite exciting

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

Transparent access of applications on Avian Flu Grid through middleware

CNIC Duckling Portal

Konkuk Glyco-M*Grid

NBCR CADD

2 – 4 March 2010 PRAGMA 18, San Diego 8

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

Virtual Screening with CSF • Virtual screening web services with remote clusters including

TeraGrid and PRAGMA Grid resources.

Virtual cluster at SDSC

AMAZON EC2

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

Kevin Dong, CNIC

Lau, Haga and Date

ViewDock TDW

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

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New OPAL-CSF4 Cloud model

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

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Parallel job scheduling in CSF4

• Two phase resource allocation in parallel job plugin– Construct virtual clusters according to job requirements– Distribute real jobs to virtual clusters

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

Social Networks and Collaborative Environment

Social Network Site Number of Users Features API Examples

Google 170 million (Gmail) Google Integrated Suite of Tools

Google Apps Engine

LinkedIn 65 million Professional Huddle/Zoho Office Online

Twitter 100 million Short MMS/SMS TwitPic

Google Wave 100,000 X 7? Upload any file Google Wave Robot

Facebook 400 million+ Social network Facebook Apps

Are these too big to fail?Utility Computing finally?

Kepler Opal Web Services Actor

Web Form for Virtual Screening Service

Cloud Computing with Amazon EC2

AutoDock Workflow

A Virtual Screening Vision Workflow

A web service

Condor pool SGE Cluster PBS Cluster

Globus Globus Globus

Application Services

Opal GUI PMV/Vision Kepler

Transparent Access Layer for Applications

Grid/Cloud ResourcesGrid/Cloud Resources

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Vision Workflow Snippet Using Opal• Two Major Steps

1. Run PDB2PQR web service.This step is skipped if an appropriate PQR file exists on the local machine.

2. Run PrepareReceptor web service.

Output is URL to PDBQT

• PDB2PQR and PrepareReceptor are skipped if an appropriate PDBQT file exists on the local machine.

– Output is PDBQT path on local machine.

Macro that runsPDB2QR web service.

Macro that runsPrepareReceptor

web service

Opal 2 for SaaS

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