PRAGMA 10 Biosciences Working Group Update Habibah Wahab, Ph.D Wilfred W. Li, Ph.D. On behalf of Karpjoo Jeong, Ph.D.

2 Key Activities Bioinformatics  mpiBLAST-G2  iGAP/Gfarm/CSF4 Avian Flu Project Metagenomics Annotation Computational Chemistry Biosciences Portal  M*Grid  NCHC Portal  My WorkSphere  Telescience  AMEXg  APAC portals Education and Training  PRIME CNIC – Kai Nan, Zhong-hua Lu  hosting 2 students from UCSD on Avian flu projects University of Zurich  PRIUS Osaka University  Kohei Ichikawa  Susumu Date  Summer Internship Program Jilin University  Zhaohui Ding  Xiaohui Wei

3 Publications [1]X. Wei, J. Jiang, W. W. Li, O. Tatebe, G. Xu, L. Hu, and J. Ju, "Implementing Data Aware Scheduling and Data Management in Gfarm using LSFtm Scheduler Plugin Mechanism," Future Generation of Computer Systems, Submitted, [2]X. Wei, Z. Ding, W. W. Li, O. Tatebe, J. Jiang, L. Hu, and P. W. Arzberger, "Grid Infrastructure for Bioinformatics Applications Based on CSF4," Future Generations of Computer Systems, Submitted, [3]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," CCGrid 2006, Singapore, [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," CCGrid, Singapore, 2006.

4 mpiBLAST-G2

5 Protein sequences Prediction of : signal peptides (SignalP, PSORT) transmembrane (TMHMM, PSORT) coiled coils (COILS) low complexity regions (SEG) Structural assignment of domains by PSI-BLAST profiles on FOLDLIB Structural assignment of domains by 123D on FOLDLIB Structural assignment of domains by WU-BLAST Data Warehouse Functional assignment by PFAM, NR assignments FOLDLIB Building FOLDLIB: PDB chains SCOP domains PDP domains CE matches PDB vs. SCOP 90% sequence non-identical minimum size 25 aa coverage (90%, gaps <30, ends<30) Domain location prediction by sequence structure info sequence info Step 1 Step 2 Step 3 Step 4 Step 5 Step 6 NR, PFAM SCOP, PDB Integrative Genome Annotation Pipeline (iGAP)

6 Gfarm virtual filesystem allows existing application to utilize distributed compute and data resources transparently and efficiently. Applications such as iGAP and their required input data may be automatically replicated to each node on demand. Distributed analysis in a virtual filesystem Gfarm File System /gfarm/eol/apps igappsiblastFoldlibNR Virtual Directory Tree Transparent distributed data access and file affinity-based application scheduling From Cluster-wide to Grid-wide environment appsdbs

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

8 CSF4 CSF4 integrate with Gfarm Gfarm Security Share Secure Key GSI Authentication  User certificate  Delegate  Proxy certificate User credentials Frontend Scheduler A Frontend Scheduler B Mutual Authentication GFS

9 Opal: Web Service Wrapper

10 Opal WSRF Operation Provider

11 M*Grid and e-Glyconjugates portal Reusable components to support a large community Comprehensive environment for molecular simulation studies

12 Computational Chemistry Use of Nimrod/G Workflow built with web services Gemstone Led by Baldridge

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15 User interface Hawk Rocks-52 ASCC Aurora IOIT-HCM Gsiftp inputs & results Globus-submit jobs Gsiftp inputs & results Globus-submit jobs Gsiftp inputs & results Globus-submit jobs Gsiftp inputs & results Globus-submit jobs Upload files/submit jobs Download & view results

16 Real Science Applications  Rational Drug Disovery of Novel Dengue Therapeutics.  Characterisation of drug binding site(s) on the DNA  Elucidating isoniazid resistance using Molecular Modelling Techniques.  Structure and function of PHA synthase Drug receptor database  Binding mode of andrographolide to Renin, HIV-1 Protease and Tyrosine kinase enzymes.  Binding of erythromycin and its relatives to ribosome. Molecular Docking and Molecular Dynamics Simulation Study.  Investigation of the Binding Properties of Some Flavonoids to Calcium using Molecular Modelling Techniques.  Molecular Modelling of Cytochrome P450 2D6. Effects of Allelic variation on the enzyme activity.  Structure based drug design of compounds derived from marine natural products.  Chemical Reactivity as a Tool to Study Carcinogenicity: Reaction between Estradiol and Estrone 3,4-Quinones Ultimate Carcinogens and Guanine.

17 New Collaboration in the Fight Against Avian Flu 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

18 Pictures

19 Participating Institutions 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

20 Participating Institutions 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

21 Breakout Session Participants USM  Habibah Wahab  Ahmad Yussof Hassan  Amin Malik Shah Abdul Majid Drug and DNA interactions Drug design UCSD/SDSC  Wilfred Li Gfarm Additional applications  Kim Baldridge GAMESS Gemstone GAMESS/APBS hybrid pipeline CNIC  Xiaoming Zhang ASCC  Hsin-Yen Chen Bioportal, MPICH-G2, LCG, Docking EGEE  Mimos  Mashkuri Yaacob  Irdawah Ab. Rahman Osaka University  Kohei Ichikawa Web services  Susumu Date TDW APAC  Rajesh Chhabra Grid portals

22 Portals Biosciences portal  Wiki already set up  PRAGMA wiki –  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

23 Communications Biosciences mailing list   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

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

25 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)

26 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  SC04 -- KISTI

27 Other Activities Summer interns  Australia: visa required  US: J-1 visa Grant applications  Applications from own funding agencies Intellectual properties  International collaborations  Standard nondisclosure agreements World community grid  Philanthropic activities

28 ISGC ~4 May Taipei EGEE Workshop  Its purpose is to introduce the EGEE project, including its goals, infrastructure, middleware and operations Symposium  It focuses on Grid core technology, Grid architecture, applications on various domains such as High Energy Physics, Bio/Medical, Digital Archive, and Atmospherics. World-Wide Grid application development, infrastructure interoperation, and collaboration would also be discussed.