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 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)

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

Opal Plugins for Popular Workflow Software

Virtualization for Bioscience Applications

MURPA 2010, Lin Wei

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

Opal Web Service Client 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

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 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

BioKnowledge Viewer GUI

University of Indonesia Working Group 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 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)

PRAGMA Institute and Related Training Activities

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

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

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

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

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