Kabir Bakie, W-Commonshttp://commons.wikimedia.org/wiki/File:Gorilla_019.jpg

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Overview

• The basic recipe: gorillas(a) Location data(b) Maps(c) Trees(d) In GenGIS(e) Variations on a theme

– GOS metagenome samples

http://commons.wikimedia.org/wiki/File:Pain_epices_DSC00141.jpg

3Mol Ecol, 2004

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Location Data!

Hmm…

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Afi Mountains

Wikipedia works too

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Dum de dum…

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Gave up on thisone...

Hand-wringing

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Create a separate sequencefile to show attributesof each individual at eachsite (leads to pie chart summaries &c)

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MapsHi ,

Thank you for your interest in Google Maps/Earth.

Unfortunately we cannot allow your proposed use. We do not permit scraping or any other sort of use of our content that is not done directly through an internet connection to Google.

You may wish to evaluate the Google Maps and Earth APIs, as they provide a means for properly using our content. More information is available at http://code.google.com/apis/maps/

Thank you for your understanding.Google Geo Permissions Team

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The (really, really, really) good news

Supports over 50 digital map formats (including tiff and jpg)

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Option 1: MapMakerFrom the GenGIS website

Saves in GeoTIFF format, no elevation data

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Option 2: ORNL DACC Webserver

This is *really* hi-res so you will want to downsample!!

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Option 3: Use GDAL with Public Data

• GTOPO30: ~1 km resolution, 33 tiles covering the whole globe. Older, but good for large swathes (precooked world maps available)

• SRTM: ~90 m resolution, 30 m for the US. Polar regions not present.

• ASTER GDEM: ~30 m in principle between 83° N and 83° S. Numerous artifacts present, apparently (we haven’t worked with these data yet)

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Option 4: ‘other’

• Private GIS collections

• Other public repositories of digital map data

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Encoding the tree

Use AUTOTREE* program to automaticallypull relationships from tree image, and buildNewick-format file.

*AUTOTREE does not actually exist

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Files done, now play.

• Basic principles of using GenGIS– Map navigation– ‘Layers’ tab– Right clicking, ‘Properties / Symbology’

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Gorilla examples

• Navigation• Location colouring and labeling• Haplogroup distributions• Manipulating trees• Movie example

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Global Ocean Sampling:Python-based manipulation of data and graphics

‘GOS.py’ – set of Python methods to do various things: subselect, visualize, analyze

drawUniqueSeqCount()subselection

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GenGIS Page

http://kiwi.cs.dal.ca/GenGIS/Main_Page