gengis presentation at vizbi 2016
TRANSCRIPT
PowerPoint Presentation
Phylogeography with GenGISRob BeikoDalhousie UniversityVizbi 2016, March 11
commons.wikimedia.org
Phylogeography
harrypotter.wikia.com
Phylogeny!
Diversity!
GeographyEnvironmentBiodiversityTREES.
webmap.ornl.govcommons.wikimedia.org
Interactive data visualization
Statistical analysis
Temporal visualizationsGeophylogeny
GenGIS
DataMap raster + vectorSamples CSVSequences CSVTrees NewickDistance matricesGenGIS architecture
Core application (C++)
Scripting interface (Python, R, RPy2)
GUI (wxPython)
OutputImagesSaved sessionsGenGIS v1: Parks et al (2009) Genome ResGenGIS v2: Parks et al (2013) PLoS ONEGraphical environment (OpenGL)
Python pluginsData retrievalData analysisWindows & Mac*
5
3D tree**********Internal nodes at geographic midpoints
Banza katydidsGenera insectorum (P. Wytsam, 1902)
2D treeInternal node layout is optimized to minimize crossings
Geographic axis
Live demo!(haha no. just kidding)
Optimizing axes
Liolaemus elongatus(Image: L. fabiani)W-Commons, Haplochromis
Remote data access / manipulationGBIF REST-like API + a bit of futzing
A. australisGlen Fergus, W-Commons
A. haastiiJohn Gerrard Keulemans Ornithological Miscellany
A. manteliiMaungatautari Ecological Island Trust
When a map is not a map
gdal.org
Ordination + ClusteringMouse gut microbiome samplesLangille et al., Microbiome, 2014
Diversity in the Human MicrobiomeData from Costello et al. (2009)
Kangaroo applesPhoto: John TannPoczai et al., Mol Biol Rep 2011
erythromycin-resistant Staphylococcus, 1980-2014Source: spatialepidemiology.net (David Aanensen, UCL)ShowSpread animation plugin
Data source: Katz et al. (2013) mBioNot exactly random sampling
Haiti cholera outbreakNepal possible source
Data source: Katz et al. (2013) mBioNot exactly random sampling
A map and a tree
The GCPD
The map we distort
A branch is less short
Geographically coupled phylogenetic distance and cartograms
Data source: Katz et al. (2013) mBio
[Where most Canadians are right now]
GenGIS
Cesium.js(par exemple)The Future..?
GenGIS developers (2007-present)
Donovan ParksTimothy MankowskiAlex KeddyBrett O'DonnellKathryn DunphySylvia ChurcherMorgan LangilleMike PorterSuwen WangHarman ClairGreg SmolynStephen BrooksChristian BlouinJacqueline Whalley (Auckland U Tech)
Finhttp://kiwi.cs.dal.ca/[email protected]@rob_beiko