tetano
Editor, Senior Moderator
Analysis and visualization of H7 influenza using genomic, evolutionary and geographic information in a modular web service
Daniel A. Janies1,?,*,
Laura W. Pomeroy2,
Jacob M. Aaronson1,
Samuel Handelman1,
Jori Hardman1,
Kevin Kawalec1,
Thomas Bitterman3,
Ward C. Wheeler4
Article first published online: 21 MAY 2012
DOI: 10.1111/j.1096-0031.2012.00401.x
? The Willi Hennig Society 2012
We have reported previously on use of a web-based application, Supramap (http://supramap.org) for the study of biogeographic, genotypic, and phenotypic evolution. Using Supramap we have developed maps of the spread of drug-resistant influenza and host shifts in H1N1 and H5N1 influenza and coronaviruses such as SARS. Here we report on another zoonotic pathogen, H7 influenza, and provide an update on the implementation of Supramap as a web service. We find that the emergence of pathogenic strains of H7 is labile with many transitions from high to low pathogenicity, and from low to high pathogenicity. We use Supramap to put these events in a temporal and geospatial context. We identify several lineages of H7 influenza with biomarkers of high pathogenicity in regions that have not been reported in the scientific literature. The original implementation of Supramap was built with tightly coupled client and server software. Now we have decoupled the components to provide a modular web service for POY (http://poyws.org) that can be consumed by a data provider to create a novel application. To demonstrate the web service, we have produced an application, Geogenes (http://geogenes.org). Unlike in Supramap, in which the user is required to create and upload data files, in Geogenes the user works from a graphical interface to query an underlying dataset. Geogenes demonstrates how the web service can provide underlying processing for any sequence and metadata database.
http://onlinelibrary.wiley.com/doi/10.1111/j.1096-0031.2012.00401.x/abstract
Daniel A. Janies1,?,*,
Laura W. Pomeroy2,
Jacob M. Aaronson1,
Samuel Handelman1,
Jori Hardman1,
Kevin Kawalec1,
Thomas Bitterman3,
Ward C. Wheeler4
Article first published online: 21 MAY 2012
DOI: 10.1111/j.1096-0031.2012.00401.x
? The Willi Hennig Society 2012
We have reported previously on use of a web-based application, Supramap (http://supramap.org) for the study of biogeographic, genotypic, and phenotypic evolution. Using Supramap we have developed maps of the spread of drug-resistant influenza and host shifts in H1N1 and H5N1 influenza and coronaviruses such as SARS. Here we report on another zoonotic pathogen, H7 influenza, and provide an update on the implementation of Supramap as a web service. We find that the emergence of pathogenic strains of H7 is labile with many transitions from high to low pathogenicity, and from low to high pathogenicity. We use Supramap to put these events in a temporal and geospatial context. We identify several lineages of H7 influenza with biomarkers of high pathogenicity in regions that have not been reported in the scientific literature. The original implementation of Supramap was built with tightly coupled client and server software. Now we have decoupled the components to provide a modular web service for POY (http://poyws.org) that can be consumed by a data provider to create a novel application. To demonstrate the web service, we have produced an application, Geogenes (http://geogenes.org). Unlike in Supramap, in which the user is required to create and upload data files, in Geogenes the user works from a graphical interface to query an underlying dataset. Geogenes demonstrates how the web service can provide underlying processing for any sequence and metadata database.
http://onlinelibrary.wiley.com/doi/10.1111/j.1096-0031.2012.00401.x/abstract