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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 HKU Hong Kong, PRC, March 2-4, 2010 PRAGMA: model for international collaboration in Technology and Science Broadening Impact of Technology Engaging Future Generations PRIME Student 2009: Jessica Hsieh, USM Scientific Drivers and Use Cases: Influenza A Virus Harris et al, PNAS, 2006 http://www.reactome.org/ http://www.wikipedia.org http://library.thinkquest.org/05aug/01479/prevention1.html 2009 H1N1 Pandemic Influenza •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) Source: http://flutracker.rhizalabs.com/ WHO Status Update Week 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/Kukmin Glyco-M*Grid NBCR CADD Relaxed Complex Scheme and Ensemble based Virtual Screening Contributed to HIV Integrase Inhibitor Development Discovery of unexpected binding site in HIV-1 Integrase using MD and AutoDock: Schames, … & McCammon, J. Med. Chem. (released on web, early 2004) “ 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). MK-0518 New Class of HIV Drugs: Merck & Co. Source: A. McCammon February, 2006 – Phase III Clinical Trials February, 2007 – Name announced: Isentress (raltegravir) October, 2007 – FDA “fast track” approval 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 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. Source: Amaro Advances in Computing Infrastructure Enables Complex Simulations of Biomolecular Systems Amaro & Li, CTMC, 2010 Opal 2 for SaaS Opal WS: Transparent Access Layer for Applications Opal App MGLTools CADD Taverna Vistrails Kepler Opal Application Services Grid/Cloud Resources Condor Condor pool CSF4 TeraGrid/PRAGMA Grid Globus PBS/SGE Clusters Opal Plugins for Popular Workflow Software 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 14 Opal MetaService: Transparent Access to Workflows and Applications 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 500 million+ Social network Facebook Apps Are these too big to fail? Utility Computing finally? New OPAL-CSF4 Cloud model • OPAL as resource manager of CSF4 • CSF4 allocate service instances of OPAL for jobs 17 PRAGMA 19 workshop, Changchun, Jilin, China, Sep.13-15, 2010. 17 2 – 4 March 2010 PRAGMA 18, San Diego 18 Integrating Visualization Workflows using Real-time bioMEdical data Streaming and visualization (RIMES) Kevin Dong, CNIC VM Replication Experiment http://goc.pragma-grid.net/wiki/index.php/VC-replication-2 • 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 User Interface AutoDock NAMD Service Manager OPAL2 Resource Manager (edu.sdsc.nbcr.opal.manager.CSFJobManager) generate RSL files Scheduling: Workflow Job CSF4 Array Job Input/Ouput Files: StageIn and StageOut MetaScheduler Grid Resources Grid Sites Biomedical CLOUD AFG VM (original) SDSC VM hosting server AFG VM (copy) NBCR VM hosting server AFG VM (copy) AIST VM hosting server ViewDock TDW Lau, Haga and Date 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? PRAGMA 20: Look Around Session • Arry Yanuar, University of Indonesia – Molecular Dynamics Simulation of disordered regions the RGK-family of small GTPase revealed no GTPase activity – Simulation often suffered from communication failure – Request: Application service for GROMACS in PRAGMA? GTP GDP GEF Small GDP GTPase Small GTP GTPase Inactive Small GDP GTPase GDI Effector Active GAP Pi Downstream sig Look Around 2 • Suntae Hwang – South Korea Kookmin University – MGrid Service on Nationwide Consortium of Supercomputing Infrastructure (PLSI) in Korea – Features: IP free, virtualized resource selection MGrid PLSI LoadLeveler Look Around Session • Day 2– NBCR CADD Pipeline Demonstration – CADD for Computer Aided Drug Discovery, Based upon the Vision workflow platform. • Nadya Williams • Requested features: – Ability to track data provenance – Ability to run workflow using own cluster • Potential collaboration – Alzheimer’s Disease -HKU Look Around – KISTI BioWorks • Bioworks workflow environment for Bioinformatics and Virtual Cell applications in Systems Biology • Seok Jeong Yu • Features: – Client server architecture – Uses Java Web Start technology – Allows users to share, edit and execute workflows – Will add PSExplorer (parameter space explorer) • Not ready for release yet Looking ahead • NBCR/SDSC and KISTI: co-development of Opal Plugin for Bioworks; scholastic exchange • UCSD and HKU: Use CADD pipeline in Alzheimer’s Disease Research • KISTI and HKU: Use Bioworks in Alzheimer’s Disease Research • UCSD and University of Indonesia: Security requirement for proprietary compound library and Opal services Looking Ahead • PRAGMA Resources: – More application services? Amber? Virtual Machines? – How can one replicate application services at own site? Is this necessary? – Data resource? Gfarm-iphone bridge is cool. Can we actually share data securely this way? – PRAGMA Institute? More hands on training on applications such as CADD for local participants? – Nimrod/K 2.0 for parameter sweep in Sapporo, Japan – Opal App for Biomedical Services – Leveraging Google App Engine and Social Network Infrastructure – Duckling Portal with Opal 2.4 support