PRAGMA 11 Biosciences Working Group Activities

1. PRAGMA 11 Biosciences Working Group Activities Raj Chhabra Wilfred W. Li, Ph.D. Habibah Wahab, Ph.D

2. Metagenomics Bioinformatics, computational biology software Gfarm/CSF4 Avian Flu Project EGEE – Academia sinica UCSD Computational Chemistry Gemstone Biosciences Portals M*Grid NCHC Portal My WorkSphere APAC portals Education and Training PRIME – Avian Flu CNIC – Kai Nan, Zhong-hua Lu Lily Cheng and Lisa Zhao PRIUS – Bioscience portal Osaka University Yohei Sawai Sanyo Seo Summer Interns -- Metascheduling Jilin University Zhaohui Ding Yuan Luo Xiaohui Wei NBCR Summer Institute Yoshio Tanaka -- AIST Osamu Tatebe -- Tsukuba Key Activities

3. Publications • [1] X. Wei, Z. Ding, W. W. Li, O. Tatebe, J. Jiang, L. Hu, and P. W. Arzberger, "GDIA: A Scalable Grid Infrastructure for Data Intensive Applications," presented at IEEE International Conference on Hybrid Information Technology, ICHIT 2006, Cheju Island, Korea, 2006. • [2] W. W. Li, S. Krishnan, K. Mueller, K. Ichikawa, S. Date, S. Dallakyan, M. Sanner, C. Misleh, Z. Ding, X. Wei, O. Tatebe, and P. W. Arzberger, "Building cyberinfrastructure for bioinformatics using service oriented architecture," presented at Sixth IEEE International Symposium on Cluster Computing and the Grid Workshops Singapore, 2006. • [3] Z. Ding, Y. Luo, X. Wei, C. Misleh, W. W. Li, P. W. Arzberger, and O. Tatebe, "My WorkSphere: Integrative Work Environment for Grid-unaware Biomedical Researchers and Applications," presented at Supercomputing Conference 2006, SC06, 2nd Grid Computing Environment Workshop, Tampa, Florida, 2006. • [4] D. Abramson, A. Lynch, H. Takemaya, Y. Tanimura, S. Date, H. Nakmura, K. Jeong, S. Hwang, J. Zhu, Z.-h. Lu, C. Amoreira, K. K. Baldridge, H.-C. Lee, C.-W. Wang, H.-L. Shih, T. Molina, W. W. Li, and P. W. Arzberger, "Deploying Scientific Applications to the PRAGMA Grid testbed: Strategies and Lessons," presented at Sixth IEEE International Symposium on Cluster Computing and the Grid, 2006. CCGrid 06., Singapore, 2006

4. Taiwan NCHC Academia sinica USA NCSA SDSC NBCR Japan AIST Titech Korea KISTI China CNIC JLU PRAGMA Gfarm Testbed

5. AIST (Japan), CNIC (China), Konkook/KISTI (Korea), UCSD/SDSC (USA), JLU (China), CGPBRI (Univ. Hawaii), USM (Malaysia) IBM World Community Grid Avian Flu Proteome Annotation and Analysis iGAP Rosetta MEME Involve students and postdocs Solving real problems using bioinformatics, molecular simulation and grid tools AutoDock Amber Gromacs GAMESS CHARMM NAMD New Collaboration in the Fight Against Avian Flu

6. SDSC/UCSD Wilfred Li Tomas Molina Cindy Zheng Peter Arzberger AIST Osamu Tatebe Hiroshi Takemiya Yusuke Tanimura Satoshi Seikiguchi Jilin University Zhaohui Ding Xiaohui Wei APAC Rajesh Chhabra Osaka University Susumu Date Kohei Ichikawa Shinji Shimojo Konkuk Karpjoo Jeong Taehoon Kim Kookmin Suntae Hwang Daeyong Heo KISTI Jae-Hyuck Kwak Young-Chul Hwang Participating Institutions

7. USM Habibah Wahab Amin Malik Sah Chan Huah Yong BII Santosh Mishra Arun Krishnan Academia sinica Hurng-Chun Lee, Chi-Wei Wang Horng-Liang Shih University of Zurich/SDSC Kim Baldridge NCHC Fang-Pang Lin Whey-Fone Tsai Weicheng Huang CNIC Zhong-Hua Lu Kai Nan Bao Ping Yan University of Wisconsin Katherine (Trina) McMahon Other Working Groups Mason Katz Yoshio Tanaka Shinji Shimojo Participating Institutions

8. USM Habibah Wahab Drug and DNA interactions Drug design UCSD/SDSC Wilfred Li Gfarm Additional applications Kayo Arima metagenomics NCHC Chang-huain Hsieh HPC – Fruitfly brain project Ye-Nu Wan SGI Hideaki Shoda – Sponsor Hiroaki Kondo FLU Julio Ibavre ASCC Hsin-Yen Chen Bioportal, MPICH-G2, LCG, Docking EGEE Osaka University Kohei Ichikawa -- Web services Susumu Date Portal Junya Seo Yohei Sawai APAC Rajesh Chhabra -- Bioportals JLU Xiaohui Wei -- CSF4 Senri-I (Senri Inter. Infor. Inst). Ryiuchi Shimizu U Canterbury Neil Gemmell U Auckland Paul Bonnington Breakout Session Participants

9. Portals • Biosciences portal • Wiki already set up • PRAGMA wiki – http://auriga.qut.edu.au/pragma • set up a PRAGMA portal and wiki • For users to try • AMEXg • One way to install • Link to all sites with available applications • Tiled Display • Much details in VMD (KB) • Could not see before • Gfarm testbed • Other technologies

10. Communications • Biosciences mailing list • pragma-biosciences@pragma-grid.org • msn, skype • Contact info listed. • Application stack • APBS • Autodock • Amber • GAMESS • Pipelines • Applications compiled for different architectures • With examples • Central site • Complaints about heterogeneity of resources • Shared installations

11. Avian flu Analysis • Two projects planned for PRIME students at CNIC • Neuraminidase inhibitor • Host selectivity • Need synopsis to refine collaborations and subprojects • Scientific discussion during breakout session – PRAGMA 11 • Discuss results • Project coordination

12. Metagenomics Annotation • Sequencing of genomes from native environmental samples • Shared software stack • Routine analysis • Use Gfarm/CSF4 for scheduling and data replication • Data services • Portal (shared infrastructure)

13. Supercomputing Demonstrations • Potential Topics • Tiled display using VMD – Kim Baldrige • BioPortal – Grid application portal • CNIC demonstration – CNGrid • GridSphere portal to Gfarm/CSF4 • Biosciences Portal. • Booth Location • SC06 – Osaka/UCSD

14. Other Activities • Summer interns • Australia: electronic business visa (up to 90 days) no hassle • US: J-1 visa • Grant applications • Applications from own funding agencies • Intellectual properties • International collaborations • Standard nondisclosure agreements • World community grid • Philanthropic activities

15. Discussion points • What is available? • BioSciences Portal –Osaka/UCSD/APAC initial stage • Autodock Portal – Taiwan- testing stage • Many other portals & tools –displayed in past • Important to know how to use them • What are the requirements • Can PRAGMA members use those? Licensing etc?

16. Discussion points.. • Different users want different software • Autodock /dock • UIUC’s NAMD • Lets extends the BioSciences portal to have a Molecular Dynamics suite • Having students is a great help • Need to be around for 4-6months • 2 months simply fly

17. Next 6 months • Resources group • Getting software stack deployed on PRAGMA resources, NAMD, Autodock, dock • CA IGTF recognized • New policy for deploying GAMA based authentication • What researchers want? • Written wishlists from researchers/institute –on the wiki (to keep it dynamic)