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Gnaneshan Public Health Bosc2008

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  • 1. Development of Web Database Applications with Open Bio Libraries in Public Health Environment Saravanamuttu Gnaneshan (Gnani) [email_address] Bioinformatics Unit / Virus Reference Department Centre for Infection Health Protection Agency, UK BOSC 2008 19 Jul 2008
  • 2. Who are we?
  • 3. HPA Centre for Infections ( CFI)
    • Objective: Prevention of Infectious Disease
    • Infectious Disease Surveillance
    • Specialist and Reference Microbiology and Microbial Epidemiology
    • Coordinating the Investigation and Cause of National and Uncommon Outbreaks
    • Helping Advise Government on the risks posed by various infections
    • Responding to International Health alert
  • 4. Bioinformatics
    • Department of Statistics, Modelling and Bioinformatics
    • Bioinformatics Unit – 10 bioinformaticians / bioinformatics scientists
    • Clientele ~400 Scientists/ Clinicians
    • Bacteria and viruses
    • Diverse data – Sequence, proteomic, expression, serology, demographic, drug resistance
  • 5. What we do?
  • 6. Few of the things we do
    • Molecular Epidemiology - online tools for microbial investigation, including organism specific databases for typing, identification and tracking the spread of infectious disease
    • Data integration of Public Health infections
    • Support services
    • Big international, European and National web systems
        • HepSEQ - Hepatitis B - http://www.hepseqresearch.org
        • WHO Measles - http://www.who-measles.org
  • 7.  
  • 8.  
  • 9.  
  • 10. How we do those?
  • 11. Our development environment
    • Open platforms – Linux, PostgreSQL, PHP, RoR, Perl, Java, BioPerl, BioRuby, etc
    • Open Bio – As glue in pipelines
    • EMBOSS suite used in all applications
    • Agile and plan driven developments
  • 12. IF (defined(we dare to say) && defined(you agree to listen)) { What we want you to do for us?; } ELSE { Silence is golden; die; }
  • 13. What we want to see in Open BIO
    • Committed development road map
    • Support and documentation issues
    • Mature tools
    • More interaction with application developers
    • Reinvigorating of projects (Bio Ruby?
    • Making closures on projects (BioPHP?)
  • 14. CFI in Colindale, London, UK Poster – E18

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