Biosciences Working Group Update

Wilfred W. Li, Ph.D., UCSD, USA

Habibah Wahab, Ph.D., USM, Malaysia

Hosted by AISTSapporo, Japan, Oct 17-20, 2011

Transparent access of applications on Avian Flu Grid through middleware

CNIC Duckling Portal

Konkuk/KukminGlyco-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

OPAL Services @ NBCR DUCKLING Portal @ CNIC

User Management

Opal Web Service Client

Application Metadata

Submit Job (Service URL)

Output URL

Metadata Cache

Job History

Application UIs

Opal Service List

Job Result

Web Service

http://opal-duckling.escience.cnhttp://ws.nbcr.net/opal2/dashboard

Wendy Fong, PRIME 2010, CNIC

Social Networks and Collaborative Environment

Are these too big to fail?Utility Computing finally?

TEXT MINING SYSTEM

InSilicoCell System architecture

Sentence selectorSentence selector

Relation extractorRelation extractor

Information elementInformation elementrecognizerrecognizer

Data handlerData handler

MetaMapMetaMap

Client Tool

NCBI dataNCBI datadownloaderdownloader

Network Network GeneratorGenerator

VisualizerVisualizer

Information Information handlerhandler

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)

Yuan Luo, IU

Application: AutoDock Virtual Screening

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