With the advent of ever-cheaper genome sequencing technologies, a wide range of organisms can now be examined at the genetic level, and biodiversity can be expressed in quantitative terms of genetic similarity and shared function. In addition to well-known genome sequencing projects, these techniques are now being applied to samples collected directly from the environment to give a cross-section of the diversity that exists at different locations in different habitats.We are developing an open source, three-dimensional geospatial information system to examine and test relationships between biodiversity, geography, and the environment. The goal is to acquire cartographic and environmental data from many sources, and overlay user-provided genomic sample sites and genetic sequences. The system includes OpenGL-based map rendering, navigation controls and a library of tools to visually compare the properties of data collected from different sample sites, as well as a command interface based on the R statistical language that allows rigourous hypothesis testing.




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Publications

Donovan H. Parks, Michael Porter, Sylvia Churcher, Suwen Wang, Christian Blouin, Jacqueline Whalley, Stephen Brooks, and Robert G. Beiko. GenGIS: A Geospatial Information System for Genomic Data. To Appear in Genome Research, accepted July, 2009. (PDF)

Jacqueline Whalley, Stephen Brooks and Robert G. Beiko. Radiť: Visualizing Taxon Properties and Parsimonious Mappings Using a Radial Phylogenetic Tree. Bioinformatics, volume 25, number 5, pp.672-673, March, 2009. (PDF)

Robert G. Beiko, Jacqueline Whalley, Suwen Wang, Harman Clair, Greg Smolyn, Sylvia Churcher, Mike Porter, Christian Blouin, and Stephen Brooks. Spatial Analysis and Visualization of Genetic Biodiversity. In Free and Open Source Software for Geospatial 2008, Cape Town, South Africa, September, 2008. (PDF)

Robert G. Beiko, Suwen Wang, Greg Smolyn, Harman Clair, Christian Blouin, Jacquelyn Whalley and Stephen Brooks. Genome Space: Mapping and Analysis of Environmental Genomic Data (Poster). Intelligent Systems in Molecular Biology (ISMB), Toronto, July 2008 (Image).

Suwen Wang, Robert Beiko and Stephen Brooks. Collapsible 3D Terrains for GIS Visualization. Proceedings of Geocomputation 2007, UK, Maynooth, September, 2007 (PDF).





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