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Biosciences Working Group Update

Biosciences Working Group Update. Wilfred W. Li, Ph.D., UCSD, USA Habibah Wahab, Ph.D., USM, Malaysia Hosted by JLU Changchun, Jilin, PRC, Sept 13-15, 2010. Scientific Driver and Use Cases. Harris et al, PNAS, 2006. http://www.reactome.org/ http://www.wikipedia.org.

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Biosciences Working Group Update

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  1. Biosciences Working Group Update Wilfred W. Li, Ph.D., UCSD, USA Habibah Wahab, Ph.D., USM, Malaysia Hosted by JLU Changchun, Jilin, PRC, Sept 13-15, 2010

  2. Scientific Driver and Use Cases Harris et al, PNAS, 2006 http://www.reactome.org/ http://www.wikipedia.org http://library.thinkquest.org/05aug/01479/prevention1.html

  3. Transparent access of applications on Avian Flu Grid through middleware CNIC Duckling Portal Konkuk Glyco-M*Grid NBCR CADD

  4. 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) MK-0518 “ 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). 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. Source: A. McCammon

  5. Ensemble-based Virtual Screening with Relaxed Complex Scheme 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. Source: Amaro

  6. Advances in Computing Infrastructure Enables Complex Simulations of Biomolecular Systems Amaro & Li, CTMC, 2010

  7. Transparent Access Layer for Applications Opal GUI PMV/Vision Kepler Application Services Grid/Cloud Resources Globus Globus Globus PBS Cluster Condor pool SGE Cluster

  8. Opal 2 for SaaS

  9. Vision Workflow Snippet Using Opal • Two Major Steps • Run PDB2PQR web service. • This step is skipped if an appropriate PQR file exists on the local machine. • 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

  10. Virtual Screening with CSF • Virtual screening web services with remote clusters including TeraGrid and PRAGMA Grid resources. Virtual cluster at SDSC AMAZON EC2

  11. New OPAL-CSF4 Cloud model • OPAL as resource manager of CSF4 • CSF4 allocate service instances of OPAL for jobs 11 PRAGMA 19 workshop, Changchun, Jilin, China, Sep.13-15, 2010.

  12. PRAGMA 18, San Diego Nornisah Mohamed, USM

  13. 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

  14. Integrating Visualization Workflows using Real-time bioMEdical data Streaming and visualization (RIMES) Kevin Dong, CNIC

  15. ViewDock TDW Lau, Haga and Date

  16. VM Replication Experimenthttp://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 AFG VM (original) VM replication AFG VM (copy) AFG VM (copy) SDSC VM hosting server AIST VM hosting server NBCR VM hosting server

  17. Milestones Update • Production use of Gfarm for sharing simulation data • Production use by PRAGMA 20 • Gfarm roll to be deployed, 48 TB • Gfarm 2.4 setup on smaller scale at the moment • Virtual machine scheduling using CSF4 • Elastic Virtual Cluster under development

  18. 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 Insitute @ PRAGMA 19

  19. PRAGMA 19 Breakout Sessions • Day 1 • Joint session with Resources WG • Prof. Kang from Konkuk Univ reported on plant pathogen structural proteomics and drug discovery activity • Expressed support for open source and free cloud services for drug discovery • Worried about the huge demand it may create on any service provider • What’s the economics model? What’s the accounting mechanism? Not something we are worrying about right now, but hopefully soon.

  20. Look around session • Day 2 • Presentation by HKU, Bao et al, on H1N1/H5N1 expression profiling using RNA-seq • Presentation by JLU, Xi et al, CSF4-ResourceManager Opal implementation • Presentation by Kookmin Univ, M*Grid

  21. Look ahead session • 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?

  22. 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?

  23. 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

  24. 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

  25. Strategies • Intra-WG: Student exchange, more regular joint meetings through green technology. • Inter-WG: Give resources on demand a real name by making demands • AFG VMs on demand in PRAGMA grid, and EC2 • Stable PRAGMA data cloud service • Stable PRAGMA compute cloud service • PRAGMA duckling portal • Engage more scientific researchers and establish more diverse use cases for cloud services

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