GenGIS presentation at Vizbi 2016
Mar. 11, 2016•0 likes•756 views
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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
- 2. commons.wikimedia.org
- 3. Phylogeography harrypotter.wikia.com Phylogeny! Diversity!
- 4. Geography Environment Biodiversity TREES. webmap.ornl.govcommons.wikimedia.org Interactive data visualization Statistical analysis Temporal visualizations Geophylogeny GenGIS
- 5. 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*
- 6. 3D tree * * * * * * * * * * Banza katydids Genera insectorum (P. Wytsam, 1902)
- 8. Live demo! (haha no. just kidding)
- 9. Optimizing axes Liolaemus elongatus (Image: L. fabiani) W-Commons, “Haplochromis”
- 10. 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
- 11. When a map is not a map gdal.org
- 12. Ordination + Clustering Mouse gut microbiome samples Langille et al., Microbiome, 2014
- 13. Diversity in the Human Microbiome Data from Costello et al. (2009)
- 14. Kangaroo apples Photo: John Tann Poczai et al., Mol Biol Rep 2011
- 15. erythromycin-resistant Staphylococcus, 1980-2014 Source: spatialepidemiology.net (David Aanensen, UCL) ShowSpread – animation plugin
- 16. Data source: Katz et al. (2013) mBio Not exactly random sampling Haiti – cholera outbreak Nepal – possible source
- 17. Data source: Katz et al. (2013) mBio Not exactly random sampling
- 18. A map and a tree The GCPD The map we distort A branch is less short Geographically coupled phylogenetic distance and cartograms
- 19. Data source: Katz et al. (2013) mBio
- 21. [Where most Canadians are right now]
- 22. Gen GIS Cesium.js (par exemple) The Future..?
- 23. 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)
- 24. Fin http://kiwi.cs.dal.ca/GenGIS rbeiko@gmail.com @rob_beiko