Transcript Biosciences-report - PRAGMA Cloud/Grid Operation Center

Biosciences Working Group Update
Wilfred W. Li, Ph.D., UCSD, USA
Habibah Wahab, Ph.D., USM, Malaysia
Hosted by AIST
Sapporo, Japan, Oct 17-20, 2011
Transparent access of applications on Avian Flu
Grid through middleware
CNIC Duckling Portal
Konkuk/Kukmin
Glyco-M*Grid
NBCR CADD
Opal Plugins for Popular Workflow Software
Virtualization for Bioscience Applications
Integration: CNIC Duckling Portal and Opal 2 Client
PRIME 2010, Brian Zhang
http://opal-duckling.escience.cn
http://ws.nbcr.net/opal2/dashboard
OPAL Services @ NBCR
Output URL
DUCKLING Portal @ CNIC
User Management
Job Result
Opal Web Service
Client
Web Service
Submit Job (Service URL)
Application UIs
Metadata Cache
Opal Service List
Application Metadata
Job History
Wendy Fong, PRIME 2010, CNIC
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?
InSilicoCell System architecture
Client Tool
TEXT MINING SYSTEM
NCBI data
downloader
MetaMap
Network
Generator
Sentence selector
Information element
recognizer
Data handler
Relation extractor
Visualizer
Information
handler
KISTI, Seok Jong Yu
BioKnowledge Viewer GUI
University of Indonesia Working Group
• Database
o
Prototype of Medicinal Plants Database and Three Dimensional Structure
of the Chemical Compounds from Medicinal Plants in
Indonesia, http://herbaldb.farmasi.ui.ac.id
Medicinal Plants
Database and Three
Dimensional Structure of
the Chemical
Compounds from
Medicinal Plants in
Indonesia, Int J Comp
Sci Issue, 2011,
8(5):180-183
Member :
Prof. Heru Suhartanto, Ph.D (High Performance and Numerical Computing)
Dr. Arry Yanuar (Pharmaceutical Chemistry)
Alhadi Bustamam, Ph.D. (GPU Computing)
Dr. Abdul Mun'im (Phytochemistry)
Hierarchical Map Reduce (HMR)
Application:
AutoDock Virtual Screening
Yuan Luo, IU
Meeting the New Challenges
• Virtualization – What does it mean to us?
– Fault Tolerance, Redundancy, Location based Access to
Services
• Production environment – Where is it? What form
should it take?
– the good old clusters, Services, EC2, VM replication
– Changing infrastructure and rise of social cloud networks
for routine file sharing, google doc, dropbox, etc.
• Collaboration – How to stay in touch better?
– PRIME, MURPA, PRAGMA Institute, NCHC, CADD
Workshop, USM, NBCR Summer Institute
– Shared Environment for Data, Services, and Interaction
PRAGMA 21 Activities
• Day 1
– WG Breakout Session 1: 13:30 – 15:00
• Improved 3D structure modeling workflow, Jason Haga,
UCSD
• CADD pipeline, Wilfred Li, NBCR/UCSD
• insilicoCell, Seok Jung Yu, KISTI
– Demo: Kevin Dong (CNIC), 15:20, today on Opal
Duckling Portal.
• Day 2
– WG Breakout Session 2: 14:45-15:45
– WG update, 16:15 – 16:45
Day 1 Breakout Session Summary
• Kevin Dong, CNIC
– Opal Duckling Portal
• User notification of job completion, and job data deletion warning
• Data cloud access, how to reduce the data management and
sharing overhead?
• Wilfred Li, NBCR/UCSD
– CADD pipeline
• Service maintenance, versioning, and virtualization
• Redundancy in application service providers, hoping Resource WG
make good progress with VM provisioing
Day 1 Summary
• Jason Haga, UCSD
– Opal-OP and Modeller for homology modeling
• Student deployment versus stable service provider via PRAGMA
• Data management, needs long term storage until no longer
necessary
• Different virtual cluster deployment method, NCHC, Rocks, Osaka
U, JLU, …
• Hsin-Yen Chen, ASGC
– Web based portal for virtual screening and analysis based
upon gLite
– Expanded resource usage through BOINC
– Virtualized computing environment under consideration
Day 1 Summary
• Seok Jong Yu, KISTI
– InsilicoCell, text mining tool for interaction pathway
• Worked with HKU on Alzheimer’s Disease
• Experimental validation through case studies, with Korean Ginseng
Corp.
• Explore web service API’s as cloud service providers
• Backend is KISTI cluster system
• Tony Cheung, University of Hong Kong (HKU)
– HKU Computer Center working with SDSC/UCSD
to deploy Opal services
– Gaussian application, MPI BLAST
Application Services
• Explore VM based service replication and
dynamic resource expansion
– Protein Electrostatic Calculations
• PDB2PQR, APBS
– Virtual Screening and Computer Aided Drug
Discovery
• AutoDock, Vina,
– MEME and other Bioinformatics applications
• Homology modeling with Modeller
– Cheminformatics applications
Data Services
• Data service that is compatible with VM based
services.
– Without data storage compatible with anticipated data size
created by VM based services, VM services are not useful
– Without good global network connection, most services
would be location based to maximize performance
– Data sharing is transient, often require ad hoc vs persistent
high bandwidth network infrastructure.
• Nextgen sequencing actually create more persistent needs for
large amount of data sharing, and data security
Service Scalability
• GPU cluster deployment for speedup of
specific types of applications
– Porting applications require domain knowledge
• Workflow systems that can select application
services wisely based upon location, and other
quality of service information
– Vision, Bioworks,
• Ease of sharing, and positive user experience
is a must
Collaboration, Education, and Training
• Engage local researchers for collaboration
– HKU and PRAGMA 20, great interaction between
HKU researchers and Biosciences WG. Thanks to
Dr. Kwan and his dedicated team
• PRAGMA Institute, NCHC, aka, SEAIP
– Fang Pang Lin, Center of Excellence of Pacific Rim
in Cyber Education and Research Collaboration
• CADD Workshop, USM
– Habibah Wahab
Others
• NBCR Summer Institute, UCSD
– Computer Aided Drug Discovery
– Scalable Computing
• PRIME, UCSD
– UCSD to Pacific Rim countries
• MURPA, Monash University
– MU students to US
Benchmarks for Success
• Joint Publications
– Co-authorship
– Use cases of service, software and infrastructure,
aka, acknowledgment
• Co-location of Workshops
– Infectious Disease Research, KISTI, PRAGMA 16,
3/09
• Attract target audience to specialized workshop as
opposed to more IT oriented PRAGMA workshop
– GEO Science Workshop, PRAGMA17, 20, 21
Benchmarks
– PRAGMA Institute on Virtualization and
Implementation, PRAGMA 18
• Unfortunately, older websites no longer exist, Duckling
portal is a really good thing, starting with PRAGMA 18.
Benchmarks
• Technology adopted
and improved,
Biosciences WG
– Duckling portal
– Gfarm
– CSF4
– Network?
– TDW, SAGE
– Opal 2, Opal OP
– Rocks and
virtualization
– gLite, globus?
– Data turbine
– Social networks?
– Workflow systems