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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

Department of Science and Technology

PHILIPPINES

rvincent@asti.dost.gov.ph

philippine e science grid program
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
philippine e science grid program3
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
objectives
Objectives
  • To enhance local availability of bioinformatics services
  • To contribute in improving research output of local bioinformatics experts
strategies
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
deployment status and plans
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
deployment status and plans8
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
infrastructure
Infrastructure
  • Network
    • PREGINET for the grid
    • Gigabit ethernet for the cluster
  • FPGA
    • BLAST
    • HMMER
    • Smith-Waterman
    • ClustalW
    • Genome Assembler
services
Services
  • Bio-Mirror node
    • >1TB data
    • http://bio-mirror.asti.dost.gov.ph
services11
Services
  • S-Star node
    • http://s-star.asti.dost.gov.ph
services12
Services
  • Collaborative Development Environment
    • http://smithy.psigrid.gov.ph
services13
Services
  • GenBank Entry Retrieval Sytem
    • under development
services14
Services
  • P2P Distribution of Biological Databases and Software
user communities
User Communities
  • Bioinformatics
    • International Rice Research Institute
    • UP Los Baños BIOTECH
    • UP Diliman CSRC
  • Biomedical Imaging
    • Ateneo de Manila University
researches
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
researches17
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
researches18
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
issues
Issues
  • Funding
  • Human Resources
  • Information Dissemination