Biosciences Working Group Update Wilfred W. Li, Ph.D., UCSD, USA Habibah Wahab, Ph.D., USM, Malaysia Hosted by UCSD San Diego, USA, March 3, 2010

Scientific Driver and Use Cases Harris et al, PNAS, 2006

Transparent access of applications on Avian Flu Grid through middleware CNIC VSDB Konkuk Glyco-M*Grid NBCR CADD

Scientific Results Newhouse et al, JACS, 2009

Recap of PRAGMA 17 – Hanoi, Vietnam, Oct 2009 Continued Software Development at member institutions – Drugscreener-G – KISTI, Korea – Grid Enabled Virtural Screening Service – ASGC, Taiwan – CADD Pipeline – NBCR, USA – WISDOM project – CNRS, EU – Glyco-M*Grid – Kookmin & Konkuk U, Korea

Progress Summary Scientific software as a Service – Continued development of application specific services – AutoDock, NAMD as Opal services – Continued development of workflows – NBCR Summer Institute training of CADD pipeline – Support for Vistrails, Vision and Kepler, Nimrod/K family Software release – Release of Opal 2.2 with condor and CSF plugins in Feb 2010

New Since PRAGMA 17 SC09 – Ability to use Condor web service interface for virtual screening using TeraGrid and OSG resources, collaboration with John McGee, RENCI – NBCR CADD pipeline is using CSF4 in production for metascheduling jobs to NBCR, TeraGrid resources, Opal- CSF4 plugin developed by Y. Luo, IU/JLU. – CNIC RIMES for dataturbine based simulation data streaming and visualization

Real-time bioMEdical data Streaming and visualization (RIMES) Kevin Dong, CNIC Dong et al, IWHGA, 2010

Milestones Update Production use of Gfarm for sharing simulation data – Production use by PRAGMA 18 not quite, delayed by hardware procurement, 48 TB Gfarm 2.3 setup on smaller scale at the moment Virtual machine scheduling using CSF4 – Demonstration by PRAGMA 19 Currently using Globus for always up instances on EC2 Condor based access achieved at PRAGMA Institute

New Challenges Virtualization – What does it mean to us? – Rock’n Rolls, on demand virtual machines, Production environment – Where is it? What form should it take? – GPU clusters, virtual machines, cloud services Most work is still done on local clusters, the desire to use the grid/Cloud is there – It’s happening, and quite exciting Collaboration – How to stay in touch better, PRIME, MURPA, research in general?

Social Networks for Scientists or Scientists using Social Networks Sociology of software engineering – Can we collaborate using Facebook? Google Wave – Can Google change how we collaborate? CDD

Biosciences Working Group Activities at PRAGMA 18 Demonstrations – NBCR CADD – Posters NA inhibitors from natural products – USM NS1 inhibitors using the RCS – UCSD/NTU Collaborative Drug Discovery – CDD, bronze sponsorship, Breakout sessions – Updates from member institutions Habibah had 17 publications last year – Discussion on Nimrod/K, Kepler use of Opal services – Joint Session with Telescience proposed for Thursday – NBCR CADD discussions – PRIME student projects

Breakout Session I Arun Datta, National University – Agile teaching technology; sequence analysis – sialyltransferase – Developing a portal for Obesity Surveillance program Hsin-Yen Chen, ASGC – Grid application platform (GAP), based upon Glite environment – AutoDock based virtual screenin – Avian flu data challenge, 1 million docking jobs – GVSS (GAP virtual screening service) – Require IGTF compliant certificate – Must become a member of a VO, TWGrid is the catchall VO. – EUAsiaGrid – Glite middleware VO for dengue fever, about 11 countries participating

Breakout Session I - 2 Thanh Truong, – Avisto, taking the technology to market, motivated – Business model  pay as you use, a course may take about 1 or 2 CPU hours, costs about $20. University may pay a pool of 100 cpu hours, used by students. – Free for high school, general chemistry usage. – Avisto – spinoff Habibah Wahab – Compounds tested from virtual screening, benchmarked with Tamiflu, commonly used DANA, also several with nm inhibition. Also checked with toxicity on MDCK cells. Hopefully by mid-June to complete testing with inhibition of viruses. – Relies on graduate students, no postdocs

Breakout Session Syed Sulaiman, USM – Animal model testing – Obtained several grants – 2 year grant, more than $1.5 million US. – Dengue fever may be becoming a more global problem Suntae Hwang – Mgrid demo, PRAGMA testbed certificate, and account for the portal – Changes since PRAGMA 17 – Reduced the steps for the number of users; RIMES integrated with MGrid