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/Kukmin Glyco-M*Grid
NBCR CADD

3. Opal WS: Transparent Access Layer for Applications
Opal App
MGLTools
CADD
Taverna
Vistrails
Kepler
Opal Application Services
Grid/Cloud Resources
Condor
CSF4
Globus
Condor pool
TeraGrid/PRAGMA Grid
PBS/SGE Clusters
Applications are first class services - users don’t have to specify paths to executables, working directories, etc
Examples of what the operations may look like
2. Security, state management, scheduling are all configured optionally
1. Jobs can even run on a Windows box - without a scheduler
3. Different services can exist in the same container - all accessible by separate URLs
4. Clients send command line arguments and input files to services (Base64 binary)

4. CADD: Opal Web Services for Biomedical Applications
Ren et al, NAR 2010, Web Server Issue
Modules supporting MD simulation and analysis, Virtual Screening, Docking, Visualization
Project management under development

5. Opal Plugins for Popular Workflow Software

6. Virtualization for Bioscience Applications

7. MURPA 2010, Lin Wei

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

9. Opal Web Service Client
OPAL NBCR
DUCKLING 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

10. Wendy Fong, PRIME 2010, CNIC

11. 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?

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

13. BioKnowledge Viewer GUI

14. University of Indonesia Working Group
Database
Prototype of Medicinal Plants Database and Three Dimensional Structure of the Chemical Compounds from Medicinal Plants in Indonesia, 
Medicinal Plants Database and Three Dimensional Structure of the Chemical Compounds from Medicinal Plants in Indonesia, Int J Comp Sci Issue, 2011, 8(5):
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)

15. PRAGMA Institute and Related Training Activities

16. 2 – 4 March 2010
PRAGMA 18, San Diego
Nornisah Mohamed, USM

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

18. 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

19. Looking ahead
NBCR/SDSC and KISTI: co-development of Opal Plugin for Bioworks; scholastic exchange
UCSD and HKU: Use CADD pipeline in Alzheimer’s Disease Research
KISTI and HKU: Use Bioworks in Alzheimer’s Disease Research
UCSD and University of Indonesia: Security requirement for proprietary compound library and Opal services

20. Looking Ahead PRAGMA Resources:
Redundant VM based Application Services Distributed Geographically for Location Based Access
Data resource, interoperability of cloud resources
Opal App for Biomedical Services – Leveraging Google App Engine and Social Network Infrastructure
Duckling Portal with Opal 2.4 support

21. PRAGMA 21 Activities Day 1 Day 2 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