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GenGIS presentation at Vizbi 2016


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Presentation about GenGIS at the "Visualizing Biological Data" (Vizbi 2016) meeting in Heidelberg, Germany. It was recommended that I include Fifty Shades of Gray in the title or description in order to increase the potential virality of the talk.

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GenGIS presentation at Vizbi 2016

  1. 1.
  2. 2. Phylogeography Phylogeny! Diversity!
  3. 3. Geography Environment Biodiversity TREES. Interactive data visualization Statistical analysis Temporal visualizations Geophylogeny GenGIS
  4. 4. Data Map – raster + vector Samples – CSV “Sequences” – CSV Trees – Newick Distance matrices GenGIS architecture Core application (C++) Scripting interface (Python, R, RPy2) GUI (wxPython) Output Images Saved sessions GenGIS v1: Parks et al (2009) Genome Res GenGIS v2: Parks et al (2013) PLoS ONE Graphical environment (OpenGL) Python plugins Data retrieval Data analysis Windows & Mac*
  5. 5. 3D tree * * * * * * * * * * Banza katydids Genera insectorum (P. Wytsam, 1902)
  6. 6. Live demo! (haha no. just kidding)
  7. 7. Optimizing axes Liolaemus elongatus (Image: L. fabiani) W-Commons, “Haplochromis”
  8. 8. Remote data access / manipulation GBIF REST-like API + a bit of futzing A. australis Glen Fergus, W-Commons A. haastii John Gerrard Keulemans – Ornithological Miscellany A. mantelii Maungatautari Ecological Island Trust
  9. 9. When a map is not a map
  10. 10. Ordination + Clustering Mouse gut microbiome samples Langille et al., Microbiome, 2014
  11. 11. Diversity in the Human Microbiome Data from Costello et al. (2009)
  12. 12. Kangaroo apples Photo: John Tann Poczai et al., Mol Biol Rep 2011
  13. 13. erythromycin-resistant Staphylococcus, 1980-2014 Source: (David Aanensen, UCL) ShowSpread – animation plugin
  14. 14. Data source: Katz et al. (2013) mBio Not exactly random sampling Haiti – cholera outbreak Nepal – possible source
  15. 15. Data source: Katz et al. (2013) mBio Not exactly random sampling
  16. 16. A map and a tree The GCPD The map we distort A branch is less short Geographically coupled phylogenetic distance and cartograms
  17. 17. Data source: Katz et al. (2013) mBio
  18. 18. [Where most Canadians are right now]
  19. 19. Gen GIS Cesium.js (par exemple) The Future..?
  20. 20. GenGIS developers (2007-present) Donovan Parks Timothy Mankowski Alex Keddy Brett O'Donnell Kathryn Dunphy Sylvia Churcher Morgan Langille Mike Porter Suwen Wang Harman Clair Greg Smolyn Stephen Brooks Christian Blouin Jacqueline Whalley (Auckland U Tech)
  21. 21. Fin @rob_beiko