Beiko gen gis2-share


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GenGIS ( presentation given by Rob Beiko at Canadian Society of Microbiologists meeting June 21, 2012

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Beiko gen gis2-share

  1. 1. GenGIS 2New approaches to understand thegeography of our microbial worldRob Beiko
  2. 2. Donovan Parks Timothy MankowskiMike Porter Brett O`Donnell
  3. 3. demo: the GenGIS environment2-24 GenGIS v1: Parks et al (2009) Genome Res
  4. 4. GenGIS v1 overview GUI (wxPython) Core Output application Saved image files (C++) Scripting interface (Python, R) Data Map – many formats (GDAL) Samples – CSV Sequences – CSV Trees - Newick Crossing minimization + statistical test Supported platforms: Windows XP, Vista, 7; OS X 10.4, 10.5, 10.6 Open source: Creative Commons Attribution – Share Alike 3.0
  5. 5. whats new in v2 GUI (wxPython) Core Output application Saved image files (C++) Save / restore Scripting interface sessions (Python, R) Data Map – many formats (GDAL) Samples – CSV Sequences – CSV Python plugins Trees - Newick External filesStability improvements, various things now work properly on the MacInterface updates (legends, data visualizations)Linear axes analysis
  6. 6. bringing map data into GenGIS• Maps: – MapMaker (included application) – Digital elevation data (, NASA Shuttle Topography data, etc.) – Images (.png, .tif, etc.)
  7. 7. three views of the LineP transect Original data: Jody Wright, Steven Hallam
  8. 8. diversity and depth
  9. 9. clustering based on Canberrabeta-diversity
  10. 10. relative abundance of SUP05
  11. 11. demo: plugins and R scripts Linear regression of group frequencies Heatmap RPy2 script Original data:10-29 Costello et al. Science 326:1694-1697
  12. 12. clustering of fecal samplesFemale subjects: F1 – F3Male subjects: M1 – M3Two sampling methods: - TP - Direct from fecesTwo time points= 4 samples per individual. Do thesesamples cluster with each other?
  13. 13. Wood Buffalo National Park • Canada’s largest National Park • UNESCO World Heritage status (Boreal Forest) • Threatened by encroaching development – Oil Sands mining (Alberta) – Metal mining (NWT) – Hydro-electric dams (Peace River, BC) • Natural resources sustain traditional use by Métis and First Nations peoplesPhotos: D Baird
  14. 14. biomonitoring 2.0 what is being collected• Benthic invertebrates (COI, 28S) – kick sample• Water (16S, 18S, 28S) – 1L volume• Soil (16S, COI, ITS, 18S, 28S, RbcL) - cores• Terrestrial arthropods (COI, 28S) – malaise / pitfall traps• All samples replicated 3 times• 5 time points in initial study• Lots of metadata (soil chemistry, flooding, etc.)
  15. 15. biomonitoring 2.0replication results – 2010 trial• fjej
  16. 16. biomonitoring 2.0sampling progress• August 2011 • Samples collected, starting analysis of sequences • traditional taxonomy where applicable (arthropods si, bacteria no)• June 2012 • Samples collected• Future sampling: August 2012, June – August 2013
  17. 17. biomonitoring 2.0our three-year mission (and beyond)• Develop robust sampling techniques for sequence- based biomonitoring• Develop and apply different approaches for assessing biodiversity (taxon-based and taxon- free), and compare their performance on WBNP data• Identify whether “reference conditions” can be established against which future samples can be compared
  18. 18. call for collaborators• Currently underway: – Combined axis tests (Many trees, one optimal gradient) – Regional tests of diversity – Canonical correlation analysis and related – Bio2.0 analysis• Goals: – Integrate with online data sources – Support more data types (especially vector data) – More plugins!
  19. 19. the long-term goalOnline data sources Analysis: with APIs -Geo gradients Automated dataset -Diversity vs. habitat + generation / -Diversity networks Local data visualization -Functional models
  20. 20. acknowledgmentsGenGIS developers (Dal)Donovan ParksMike Porter LineP (UBC)Timothy Mankowski Jody WrightBrett ODonnell Steven HallamKathryn Dunphy Bio2.0Sylvia ChurcherMike Porter Mehrdad Hajibabaei (Guelph)Suwen Wang Donald Baird, Wendy Monk (UNB)Harman Clair Brian Golding (McMaster)Greg Smolyn Jeff Shatford (Parks Canada)Stephen BrooksChristian BlouinJacqueline Whalley (Auckland U Tech)
  21. 21. New Zealand fungus beetle (Agyrtodes labralis)COI phylogenyEcological niche modelling suggests Marske et al. Mol Ecol (2009)several glacial refugia, phylogenies Data shown in GenGISsuggest transalpine migration
  22. 22. map
  23. 23. locations
  24. 24. sequence summaries
  25. 25. tree vs geography
  26. 26. axes test
  27. 27. body site data
  28. 28. linear regression
  29. 29. heatmaps using R