Biosciences Working Group Update
Wilfred W. Li, Ph.D., UCSD, USA
Habibah Wahab, Ph.D., USM, Malaysia
Hosted by JLUChangchun, 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 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
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
Opal 2 for SaaS
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 runsPDB2QR web service.
Macro that runsPrepareReceptor
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
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New OPAL-CSF4 Cloud model
PRAGMA 19 workshop, Changchun, Jilin, China, Sep.13-15, 2010.
2 – 4 March 2010 PRAGMA 18, San Diego 12
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
Lau, Haga and Date
ViewDock TDW
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
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
» What’s the economics model? What’s 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