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.

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
*
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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