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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 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.

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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 AIST Sapporo, Japan, Oct 17-20, 2011

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

  3. Opal Plugins for Popular Workflow Software

  4. Virtualization for Bioscience Applications

  5. Integration: CNIC Duckling Portal and Opal 2 Client PRIME 2010, Brian Zhang

  6. http://opal-duckling.escience.cn http://ws.nbcr.net/opal2/dashboard OPAL Services @ NBCR DUCKLING Portal @ CNIC Output URL User Management Job Result Opal Web Service Client Web Service Application UIs Submit Job (Service URL) Metadata Cache Opal Service List Job History Application Metadata

  7. Wendy Fong, PRIME 2010, CNIC

  8. Social Networks and Collaborative Environment Are these too big to fail? Utility Computing finally?

  9. InSilicoCell System architecture Web Services (OPAL2) Client Tool TEXT MINING SYSTEM NCBI datadownloader MetaMap Network Generator Information element recognizer Sentence selector Visualizer Relation extractor Data handler Information handler KISTI, Seok Jong Yu

  10. BioKnowledge Viewer GUI

  11. University of Indonesia Working Group • 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 Database Prototype of Medicinal Plants Database and Three Dimensional Structure of the Chemical Compounds from Medicinal Plants in Indonesia, http://herbaldb.farmasi.ui.ac.id 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)

  12. Hierarchical Map Reduce (HMR) Application: AutoDock Virtual Screening Yuan Luo, IU

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  21. 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

  22. 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

  23. 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

  24. 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.

  25. 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

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