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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

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