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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 Department of Science and Technology PHILIPPINES rvincent@asti.dost.gov.ph. Philippine e-Science Grid Program.

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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!

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