Development of Web Database Applications  with Open Bio Libraries  in Public Health Environment Saravanamuttu Gnaneshan (G...
Who are we?
HPA Centre for Infections ( CFI) <ul><li>Objective: Prevention of Infectious Disease </li></ul><ul><li>Infectious Disease ...
Bioinformatics  <ul><li>Department of Statistics, Modelling and Bioinformatics </li></ul><ul><li>Bioinformatics Unit – 10 ...
What  we do?
Few of the things we do <ul><li>Molecular Epidemiology - online tools for microbial investigation, including organism spec...
 
 
 
How we do those?
Our development environment  <ul><li>Open platforms – Linux, PostgreSQL, PHP, RoR, Perl, Java, BioPerl, BioRuby, etc </li>...
IF (defined(we dare to say) &&  defined(you agree to listen)) { What  we want you to do for us?; } ELSE { Silence is golde...
What we want to see in Open BIO <ul><li>Committed development road map </li></ul><ul><li>Support and documentation issues ...
CFI in Colindale, London, UK  Poster – E18
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Gnaneshan Public Health Bosc2008

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Gnaneshan Public Health Bosc2008

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