1. A rapid visualization pipeline for the 2009 A/H1N1 influenza pandemic Donovan Parks Norm MacDonald Rob Beiko

2. A little biology Motivation Data acquisition pipeline GenGIS: a genomic GIS framework ExamplesOutline1/10 Photo obtained from commons.wikimedia.org

3. H1N1 Biology 2/10 Modified photo from commons.wikimedia.org

4. Motivation3/10 Move from reactive to preventive health strategy Increased sampling requires automated tools PandemicYearDeaths worldwide (est.) Fatality rate Spanish flu1918-1920 to 100 million> 2.5% Asian flu1956-582 million< 0.1% Hong Kong flu1968-691 million< 0.1% Seasonal fluEvery year0.25-0.5 million< 0.1%

5. Pipeline Overview 4/10

6. Data Acquisition Pipeline 5/10

7. SeqMonitor6/10 http://ratite.cs.dal.ca/SeqMonitor/

8. GenGIS: A Genomic GIS Framework 7/10

9. Global Genetic Diversity of NA 8/10

10. NA Polymorphism 9/10 October 19, 2009

11. Conclusions Global, continuous sequencing of infectious diseases would allows us to implement preventive health strategies. Automated tools will be necessary to provide analyses to inform such policies. 10/10

12. Further Information SeqMonitor: http://ratite.cs.dal.ca/SeqMonitorhttp://ratite.cs.dal.ca/SeqMonitor – MacDonald, N. J., Parks, D. H., and Beiko, R. G. SeqMonitor: Influenza Analysis Pipeline and Visualization. PLoS Currents: Influenza. 23 September 2009: RRN1040. GenGIS: http://kiwi.cs.dal.ca/GenGIShttp://kiwi.cs.dal.ca/GenGIS – Parks, D. H., Porter, M., Churcher, S., Wang, S., Blouin, C., Whalley, J., Brooks, S., and Beiko, R. G. GenGIS: A geospatial information system for genomic data. Genome Res. July 27, 2009. – Parks, D. H., MacDonald, N. J., and Beiko, R. G. Tracking the evolution and geographic spread of influenza A. PLoS Currents: Influenza. 21 August 2009: RRN1014.