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Web Portal Service on Open Bioinformatics Grid (OBIGrid)

Life Science Grid Symposium Web Portal Service on Open Bioinformatics Grid (OBIGrid) Konagaya Akihiko RIKEN GSC Bioinformatics Group Outline OBIGrid and Bioinformatics Applications OBISgd: Scalable Genome Database OBITco: Thermus Thermophilus Cyber Outlet

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Web Portal Service on Open Bioinformatics Grid (OBIGrid)

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  1. Life Science Grid Symposium Web Portal Service on Open Bioinformatics Grid (OBIGrid) Konagaya Akihiko RIKEN GSC Bioinformatics Group

  2. Outline • OBIGrid and Bioinformatics Applications • OBISgd: Scalable Genome Database • OBITco: Thermus Thermophilus Cyber Outlet • OBIYagns: Yet Another Gene Network Simulator

  3. OBIGrid (Open Bioinformatics Grid) PC Cluster PC Cluster • Isolation by VPN+FW • Authentication by Globus • Connection via Internet DB search program XMLDB Cell simulation program VPN-FW VPN-FW Internet Site-A Site-C VPN-FW VPN-FW node with MDM Current Status (2003 March) Academic 11・ Company 9・NRI 5CPU203nodes115 Genome DB mirror Seq. anal. program MD simulation program Site-B Site-D

  4. OBIEnv: Bioinformatics Environment (Sato) Resource Searcher • Single Account • Script Prog. Env. • Parallel BLAST/DB Job Acceptance Jobs Node Search Node Set Results Globus Tool Kit Globus Tool Kit Resource Manager Job Dispatcher Scanning Environment Job Execution Workers Local Authentification Portal Application My Script DB HW SW Mapping of Local user account To Grid User Account Or Public User Account OBIEnv Users Other local users not permitted to OBIEnv Access

  5. Web Applications

  6. Issues in Integrated Database • How to deal with huge datasets? Scalable XML Database Search System • How to deal with heterogeneous datasets? Computational Pipeline and Gene Annotation Support System

  7. Issues in Cell Simulation • How to estimate unknown parameters? Differential Equation Simulation + Genetic Algorithm Requires Enormous Computation • How to validate simulation models? Biological Experiments/ Literature Information Infrastructure for data/model/knowledge sharing

  8. OBISgd: Distributed XML DB Browser XMLDB XMLDB Distributed Index Search Servers XMLDBｓ index search index search index search index search ＤＤＢＪ－ＸＭＬ ＳＯＡＰ Web portal Perl API JAVA API • Scalability • Quick Response • High reliability

  9. ＤＤＢＪ－XML DBｓ ＤＤＢＪ－XML DBｓ ＤＤＢＪ－XML DBｓ Search index Search index Search index Search index ＰｏｓｔｇｒｅＳＱＬ ＰｏｓｔｇｒｅＳＱＬ ＰｏｓｔｇｒｅＳＱＬ ＰｏｓｔｇｒｅＳＱＬ File Server System Configuration Parallel Search Engine ＳＯＡＰ Server Ｗｅｂ Server Parameter：AB000100 getXML_DDBJEntry Ａｐａｃｈｅ ＤＤＢＪ－ＸＭＬ ＳＯＡＰ Ｔｏｍｃａｔ ＸＳＬＴ XML SELECT * FROM bct1_3 where val like 'BCT%' ＸＳＬ Web Browser Candidate Entry List HTML

  10. OBITco: Thermus T. Cyber Outlet Biological Experimental Data Integration of All Information Necessary for Whole Cell Simulation Experimental Analysis Data Annotation on Molecular Function Annotation by Researchers Automatic Annotation >S53477 PIR2 release 73.00 MAAIRDYKTALDLTKSLPRPDGLSVQELMDSKIRGGLAYNDFLILPGLVD FASSEVSLQTKLTRNITLNIPLVSSPMDTVTESEMATFMALLDGIGFIHH NCTPEDQADMVRRVKNYENGFINNPIVISPTTTVGEAKSMKEKYGFAGFP VTADGKRNAKLVGAITSRDIQFVEDNSLLVQDVMTKNPVTGAQGITLSEG NEILKKIKKGRLLVVDEKGNLVSMLSRTDLMKNQKYPLASKSANTKQLLW GASIGTMDADKERLRLLVKAGLDVVILDSSQGNSIFQLNMIKWIKETFPD LEIIAGNVVTKEQAANLIAAGADGLRIGMGTGSICITQKVMACGRPQGTA VYNVCEFANQFGVPCMADGGVQKHWSYYYQSFGSWFFYCYDGWYVGRYYR ITR Genome Sequence Database 3D structure database Protein Interaction Database Literature Database

  11. System overview Access Manager SSL connection OBIGrid network Thermus server Secure remote annotation by biologists using SSL on Web Browser

  12. Annotation system Top page Menu page Annotation page

  13. ORF Prediction • 4 programs were used to predict ORF regions in contig sequences. • handai (original annotation done by Osaka U.) • bdgf (BioDictionary Gene Finding, by T.Shibuya, IBM) [1] • getorf1 (with standard genetic code) [2] • getorf2 (with bacterial genetic code) • getorf is ORF finding and extracting program (part of EMBOSS packages) [1] Shibuya,T., Rigoutsos, I., “Dictionary-driven prokaryotic gene finding”, NAR. 30: pp.2710-2725, 2002 [2] http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Apps/getorf.html

  14. OBIYagns: Cell Simulation Environment EGF receptor EGF SOS PI3K Grb2 PKC Shc Grb2 SOS PLC RAS NF-kappaB MAPKKKs STAT3 STAT1 CyclinD1/cdk4/6 MAPKKs STAT1 Rb E2F Rb-p STAT3 MAPKs E2F MAPKs STAT1 E2F STAT3 AP-1 Elk-1 ＤＮＡＤＮＡＤＮＡＤＮＡＤＮＡＤＮＡ Signal Transduction • ODE Solver for Stiff Problems • Unknown Parameter Estimator Solver Web portal Mathematical Modeling Perl API JAVA API Cell Cycle

  15. System Configuration Web browser • Unknown Parameter Estimation by Real-code Genetic Algorithm • (Embarrassing) Parallel Execution of ODE solvers Remote Execution PC Cluster Web server GA ODE solver ODE solver Task Manager MPI communication ODE solver ODE solver ODE solver Results of Parameter Estimation ODE solver Expandable to GAGrid (Ono)

  16. Operation ② ① ⑥ ⑦ ③ ④ ⑤ • Selection of reaction type; • mass-action, Michaelis-Menten • Input of kinetic parameters • Input of initial concentrations of reactions • Input of fitting data • Input of fitting expressions • Input of GA parameters, and run GA program • Display result of parameter estimation

  17. Summary • OBIGrid is practical grid computing test bed over the Internet. • 20 sites are connected via VPN and • 203 cpus/ 115 nodes are available. • Some Web Applications are operational • and frameworks for web portal sites and • computational pipelines are under development.

  18. titles omitted Staff OBIGrid Contributors Kyoko Hirukawa（JAIST），Hiroko Furuno，Sonoko Endo, Keiko Satake（GSC） VPN/Globus net Hiroyuki Umeda（IBM） OBIEnv/OBISgd Kenji Sato, Xavier Defago（JAIST）, Shinichi Tsuji, Yasuhiko Nakajima（HNES） Makoto Taiji, Tetsu Narumi, Noriyuki Futatsugi, Naoki Takada（GSC）, Tomoyuki Yamamoto（JAIST） OBIMde OBITco/ OBIYagns Fumikazu Konishi, Akinobu Fukuzaki, Ryo Umetsu, Noriko Mito, Aki Hasegawa, Mariko Hatakeyama, Kaori Ide（GSC） Seiki Kuramitsu, Shigeyuki Yokoyama, Ryoji Masui, Noriko Nakai（Structurome） Shuhei Kimura（GSC）, Takuji Kawasaki（FUJI RIC） Grid WG of Japan Committee on High-Performance Computing for Bioinformatics Masahiro Okamoto（Kushu Uni.）, Isao Ono（The Uni. Of Tokushima）, Takahiro Koita（OSU）, Hiroshi Someya（ISM）, Keisuke Tanaka（Titech）, Hideki Nakada（ AIST, Titech）, Tsuneo Nakanishi（ Kushu Uni.）, Tomoyuki Hiroyasu（Dosisha Uni.）, Akira Fukuda（ Kushu Uni.）, Satoshi Matsuoka（Titech）, Masayuki Yamamura（ Titech）, Tetsushi Yada（HGC), Satoshi Miyazaki（DDBJ）, Asao Fujiyama（NII）, Morikazu Nakamura（Uni. Of the Ryukyus）, Hiroyuki Kurata（KIT） Grid WG of Initiative for Parallel Bioinformatics MITSUBISHI RESEARCH INSTITUTE, Inc. RIKEN Yokohama Institute RIKEI Corporation ESCA, Co. INTEC Web and Genome Informatics Corporation CTC LABORATORY SYSTEMS Corporation NIPPON SHINYAKU Co,. Ltd. NEC Corporation FUJI Research Institute Corpration FUJITSU Limited BEST SYSTEMS Inc NIPPON TELEGRAPH AND TELEPHONE WEST Corporation NTT ＤＡＴＡ Corporation Cognitive Research Laboratories, Inc. Hewlett-Packard Japan, Ltd. National Institute of Advanced Industrial Science and Technology SURIGIKEN Co., Ltd.SUMISHO Eelectronics Co., Ltd. NEC Software Hokuriku, Ltd. IBM Japan, Ltd. Leader Akihiko Konagaya (JAIST, Riken)

  19. OBIGrid http://obigrid.org End

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