PRAGMA Institute on PRAGMA 19 Wilfred W. Li, Ph.D., UCSD, USA Xiaohui Wei, Ph.D., JLU, PRC Hosted by JLU Changchun, Jilin, PRC, Sept 13, 2010 Avian Flu Grid: Transition from Grid to Cloud Computing

Scientific Driver and Use Cases 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 Trials February, 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 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. 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? – Rockn 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 – Its 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 Diego8 Nornisah Mohamed, USM

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 13 New OPAL-CSF4 Cloud model PRAGMA 19 workshop, Changchun, Jilin, China, Sep.13-15, 2010.

14 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 SiteNumber of UsersFeaturesAPI Examples Google170 million (Gmail)Google Integrated Suite of Tools Google Apps Engine LinkedIn65 millionProfessionalHuddle/Zoho Office Online Twitter100 millionShort MMS/SMSTwitPic Google Wave100,000 X 7?Upload any fileGoogle Wave Robot Facebook400 million+Social networkFacebook 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 poolSGE Cluster PBS Cluster Globus Application Services Opal GUIPMV/VisionKepler Transparent Access Layer for Applications Grid/Cloud Resources

22 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 runs PDB2QR web service. Macro that runs PrepareReceptor web service

Opal 2 for SaaS

VM Replication Experiment 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