Presentation on theme: "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."— Presentation transcript:
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 http://www.reactome.org/ http://www.wikipedia.org http://library.thinkquest.org/05aug/01479/prevention1.html Harris et al, PNAS, 2006
Transparent access of applications on Avian Flu Grid through middleware CNIC Duckling Portal Konkuk Glyco-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 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
9 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
Virtual Screening with CSF Virtual screening web services with remote clusters including TeraGrid and PRAGMA Grid resources. Virtual cluster at SDSC AMAZON EC2
OPAL as resource manager of CSF4 CSF4 allocate service instances of OPAL for jobs 11 New OPAL-CSF4 Cloud model PRAGMA 19 workshop, Changchun, Jilin, China, Sep.13-15, 2010.
2 – 4 March 2010 PRAGMA 18, San Diego12 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
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 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
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
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
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 » Whats the economics model? Whats the accounting mechanism? Not something we are worrying about right now, but hopefully soon.
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
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?
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
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