gnaneshan public health bosc2008
TRANSCRIPT
Development of Web Database Applications
with Open Bio Libraries in Public Health Environment
Saravanamuttu Gnaneshan (Gnani)[email protected]
Bioinformatics Unit / Virus Reference DepartmentCentre for Infection
Health Protection Agency, UK
BOSC 200819 Jul 2008
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Who are we?
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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
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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
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What we do?
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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
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How we do those?
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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
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IF (defined(we dare to say) && defined(you agree to listen)) {What we want you to do for us?;
}ELSE {
Silence is golden;die;
}
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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?)
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CFI in Colindale, London, UK
Poster – E18