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Bioinformatics Development in the Philippines Rey Vincent P. Babilonia Advanced Science and Technology Institute Departm PowerPoint Presentation
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Bioinformatics Development in the Philippines Rey Vincent P. Babilonia Advanced Science and Technology Institute Departm

Bioinformatics Development in the Philippines Rey Vincent P. Babilonia Advanced Science and Technology Institute Departm

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Bioinformatics Development in the Philippines Rey Vincent P. Babilonia Advanced Science and Technology Institute Departm

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  1. Bioinformatics Development in the Philippines Rey Vincent P. Babilonia Advanced Science and Technology Institute Department of Science and Technology PHILIPPINES rvincent@asti.dost.gov.ph

  2. Philippine e-Science Grid Program • Aims to establish a grid infrastructure in the Philippines that will: • Enable collaborative research activities among local and regional educational and research institutions, and • Provide distributed services to general users such as national institutions that will use the grid to deliver advanced services

  3. Philippine e-Science Grid Program • Project 1: Boosting Grid Computing Using Reconfigurable Hardware Technology • Project 2: Developing a Federated Geospatial Information System for Hazard Mapping and Assessment • Project 3: Boosting Social and Technological Capabilities for Bioinformatics Research

  4. Project 3:Boosting Social and Technological Capabilities for Bioinformatics Research (PBS)‏

  5. Objectives • To enhance local availability of bioinformatics services • To contribute in improving research output of local bioinformatics experts

  6. Strategies • Provide rapid access to major biological sequences and structure database • Provide web hosting service for bioinformatics programs to local researchers • Enhance the expertise of local researchers in bioinformatics through trainings

  7. Deployment Status and Plans • Year 1 • Build new HPC facility • Install BioBoost addons and software • Connect with UP Diliman CSRC, IRRI and UP Los Baños BIOTECH • Install grid-accessible bioinformatics solutions • Develop Web-based search engine and interface • Create course materials • Conduct capability building for local researchers in bioinformatics

  8. Deployment Status and Plans • Year 1 (cont.)‏ • Publish paper • Mirror major biological sequence and structure databases • Year 2 • Conduct capability building for local researchers in bioinformatics • Deploy 3D visualization facility • Publish paper

  9. Infrastructure • Network • PREGINET for the grid • Gigabit ethernet for the cluster • FPGA • BLAST • HMMER • Smith-Waterman • ClustalW • Genome Assembler

  10. Services • Bio-Mirror node • >1TB data • http://bio-mirror.asti.dost.gov.ph

  11. Services • S-Star node • http://s-star.asti.dost.gov.ph

  12. Services • Collaborative Development Environment • http://smithy.psigrid.gov.ph

  13. Services • GenBank Entry Retrieval Sytem • under development

  14. Services • P2P Distribution of Biological Databases and Software

  15. User Communities • Bioinformatics • International Rice Research Institute • UP Los Baños BIOTECH • UP Diliman CSRC • Biomedical Imaging • Ateneo de Manila University

  16. Researches • Application of bioinformatics to microbial biotechnology • Organization of protein and DNA databases of microorganisms relevant to food safety and functional foods • Establishing a molecular marker database for Actinomycetes relevant to antibiotic production • Molecular and protein characterization of commercially important locally-isolated microbial strains held at the Philippine National Collection of Microorganisms

  17. Researches • Strain improvement of Bacillus sp. for Xylanase production • Development of recombinant Zymomonas mobilis for conversion of xylose to ethanol • Bioinformatic Analysis of Mycorrhizal Fungi and Associated Microbial Communities in Different Marginal Areas for the Enhancement of Agricultural and Forestry Productivity • Molecular Characterization and Identification of Effective Bacterial Endophytes as Bio-inoculant for Papaya

  18. Researches • Fingerprinting of nitrogen-fixing endophytic bacteria, an inoculant for Jatropha curcas L. as biodiesel source • Data warehousing of microbial information databases • Rice and Climate Change Consortium • High-resolution regional climate modeling under different climate change scenarios of Central Luzon, Philippines

  19. Issues • Funding • Human Resources • Information Dissemination

  20. Thank you!