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Natjaree Preechaveerakul 1 , Unitsa Sungket 3 , Kasikrit Damkliang 1 ,

Working on Thailand’s BioGrid Infrastructure and myGrid Technology. Natjaree Preechaveerakul 1 , Unitsa Sungket 3 , Kasikrit Damkliang 1 , Pichaya Tandayya 1, 2 , Amornrat Phongdara 3 and Pitipol Meemak 3 PSU Grid Centre, Prince of Songkla University 1

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Natjaree Preechaveerakul 1 , Unitsa Sungket 3 , Kasikrit Damkliang 1 ,

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  1. Working on Thailand’s BioGrid Infrastructure and myGrid Technology Natjaree Preechaveerakul 1,Unitsa Sungket 3,Kasikrit Damkliang 1, Pichaya Tandayya 1, 2, Amornrat Phongdara3andPitipol Meemak 3 PSU Grid Centre, Prince of Songkla University 1 Department of Computer Engineering, Prince of Songkla University 2 Center for Genomics and Bioinformatics Research, Prince of Songkla University 3

  2. Naratted by Dr. Arnon Rungsawang Dept. of Computer Engineering Kasetsart University Thai National Grid Center APAN26 - 6 Aug 2008, Queenstown, NZ

  3. BioGrid Team Prince of Songkla University • Computer Engineering Department, Faculty of Engineering • Center for Genomics and Bioinformatics Research, Faculty of Science BioGrid Project APAN26 - 6 Aug 2008, Queenstown, NZ

  4. Funding This project has been funded by Thai National Grid Center (TNGC) under Software Industry Promotion Agency (SIPA). BioGrid Project APAN26 - 6 Aug 2008, Queenstown, NZ

  5. Objectives • To build BioGrid infrastructure for Thailand • To build a research network in Bioinformatics • To navigate the Grid usage in Bioinformatics • To build new researchers in Bioinformatics • To promote the myGrid technology BioGrid Project APAN26 - 6 Aug 2008, Queenstown, NZ

  6. Accomplishments • Software Installation and Support: • MPIBlast • Bio Roll • Bio Portal • Taverna • Training: related workshops BioGrid Project APAN26 - 6 Aug 2008, Queenstown, NZ

  7. Background: Bioinformatics • Apply computer technology to biological information • gather, store, analyze and integrate biological and genetic information such as nucleotide and amino acid sequences • Example applications: • gene-based drug discovery and development • Multidiscipline: • Biology, Computer Science, Mathematics and Information Technology BioGrid Project APAN26 - 6 Aug 2008, Queenstown, NZ

  8. MPIBlast http://www.mpiblast.org/ • A Message Passing Interface - Basic Local Alignment Search Tool, • Uses the parallel implementation of NCBI BLAST, • Efficiently utilizes distributed computational resources through database fragmentation, query segmentation, intelligent scheduling, and parallel I/O, • Improves NCBI BLAST performance by several orders of magnitude while scaling to hundreds of processors. BioGrid Project APAN26 - 6 Aug 2008, Queenstown, NZ

  9. MPIBlast Databases on TNGC The below databases are on service on the Tera Cluster of the Thai National Grid Center. nr: Non-redundant protein sequence database nt: Not non-redundant nucleotide database Etc. BioGrid Project APAN26 - 6 Aug 2008, Queenstown, NZ

  10. Bio Portal on TNGC • The pioneer portal on the the Tera Cluster of the Thai National Grid Center uses • Gridsphere portal framework • MPI-Blast service http://tera.thaigrid.or.th:8081/gridsphere Contact: support@psu-grid.coe.psu.ac.th BioGrid Project APAN26 - 6 Aug 2008, Queenstown, NZ

  11. Bio Grid Infrastructure Bio Grid services include web services, portals, command line tools. BioGrid Project APAN26 - 6 Aug 2008, Queenstown, NZ

  12. Taverna BioGrid Project APAN26 - 6 Aug 2008, Queenstown, NZ

  13. Taverna • Free software tool • Support various platform • For designing and executing workflows http://taverna.sourceforge.net/ BioGrid Project APAN26 - 6 Aug 2008, Queenstown, NZ

  14. What is a Workflow? A set of components and relations between them used to define a complex process from simple building blocks BioGrid Project APAN26 - 6 Aug 2008, Queenstown, NZ

  15. Fussy Old Cut-and-paste Method • Various services and databases are distributed and so different in standards • Cutting and Pasting between web pages in each window of browser needs labor, iteration and is difficult to verify • Can not apply to a large scale of research • nor fulfill the scientific expectation BioGrid Project APAN26 - 6 Aug 2008, Queenstown, NZ

  16. Advantages of Using Workflows • High-level abstraction • Easier to understand and modify. • Easier to describe and discuss with others. • Describes what you want to do, not how to do it. • Automation • Sharing and re-use BioGrid Project APAN26 - 6 Aug 2008, Queenstown, NZ

  17. Components in Taverna • Reusable building block which performs some well defined function within a process, • Computational resource accessible via the internet or on user's local work station, web services, command line tool, and perl scripts BioGrid Project APAN26 - 6 Aug 2008, Queenstown, NZ

  18. Our Work: Thai Taverna documents • Installation • Composition • Plugins • Example • Etc. http://biogrid.coe.psu.ac.th BioGrid Project APAN26 - 6 Aug 2008, Queenstown, NZ

  19. Taverna and BioGrid Workshops Speakers: • Prof. Dr. Andy Brass, and Dr. Katy Wolstenkroft from University of Manchester • Assoc. Prof. Dr. WasanJantratit and AkawatPasomsap from Mahidol University (MU) • Asst.Prof.Dr. PichayaTandayya and UnitsaSungket from Prince of Songkla University (PSU) • Assoc. Prof. Dr. ChokchaiLeangsuksun, from Louisiana Tech University (LSU) Venues: PSU, MU, CMU, KU BioGrid Project APAN26 - 6 Aug 2008, Queenstown, NZ

  20. Demo • Bio Portal • Taverna BioGrid Project APAN26 - 6 Aug 2008, Queenstown, NZ

  21. Software and Services Provided • MPIBlast and Bio Roll on the Tera Cluster and at the clusters of Thai National Grid Members • Command line service • Bio Portal on the Tera Cluster of TNGC • MPIBlast service • Taverna on the Tera Cluster and at the clusters of Thai National Grid Members • Local Web services at any cluster for faster processing in Taverna workflow • Taverna manual document in Thai BioGrid Project APAN26 - 6 Aug 2008, Queenstown, NZ

  22. List of Software • Command line service • MPIBlast • FASTA • ClustalW • Emboss • Glimmer • biopython • MrBayes • Phylip • Bio Portal • MPIBlast service • Taverna • Local web services for Taverna BioGrid Project APAN26 - 6 Aug 2008, Queenstown, NZ

  23. Examples of BioGrid’s Usage • Pharmacogenomics • shrimp SNPs analysis • Statistic Computation on Genome Wide Association Study BioGrid Project APAN26 - 6 Aug 2008, Queenstown, NZ

  24. Acknowledgements • Prof. Dr. Carole Goble and myGrid team members, School of Computer Science at the University of Manchester for Taverna Training • Yossatorn Phumisut from Manakorn University for Grid Sphere Knowledge BioGrid Project APAN26 - 6 Aug 2008, Queenstown, NZ

  25. Information BioGrid Project APAN26 - 6 Aug 2008, Queenstown, NZ

  26. Thank You. All questions should be directed to Dr. Putchong U. or Dr. Pichaya T. APAN26 - 6 Aug 2008, Queenstown, NZ

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