GenGIS Tutorials

We have put together a few tutorials to get you quickly started with GenGIS.

Tutorial 0: Obtaining Custom Digital Elevation Maps (DEM)

The simple way to obtain DEMs suitable for use in GenGIS is described here. An older set of instructions on how to manually contruct a custom DEM is available here. You can also obtain 2D maps compatible with GenGIS using MapMaker.

Tutorial 1: Banza Katydids of the Hawaiian Islands

Geophylogeny of Banza katydids from the Hawaiian Islands.

In this tutorial, we consider the phylogenetic tree of Banza katydids (acoustic insects) from the Hawaiian Islands recently recovered by Shapiro et al., 2006. This tutorial gives an overview of the GenGIS interface, demonstrates how to load data, and illustrates how to change the visual properties of a map, location markers, and trees. The tutorial concludes with an analysis which suggests geography has had a substantial influence on the evolution of Banza katydids.

• Banza Katydid tutorial
• Stream video tutorial
• Download Banza Katydid data set

Tutorial 2: Marine Microbial Communities from the Atlantic Seaboard

Here we examine samples collected as part of the Global Ocean Sampling expedition (Rusch et al., 2007) in order to investigate the influence of environmental factors on the composition of microbial communities from marine ecosystems. This tutorial demonstrates how to load data, illustrates how to change visual properties, presents a detail analysis of the geographic structure of these microbial communities, and examines the distribution of taxa within these samples.

• GOS tutorial
• Stream video tutorial
• Download GOS data set

Tutorial 3: Microbial diversity at 28 human body sites

Costello et al. (2009) collected microbial marker gene samples from 28 distinct human body sites to assess variation across sites, broad cateogories of sites (for instance, skin vs. gut) and through time. The following tutorial shows how to use plugins to perform statistical tests and generate visualizations, and how roll your own analysis scripts using Rpy2.

• Body Location tutorial
• Download body site data set and analysis script

Tutorial 4: The Ensatina eschscholtzii ring species

The Ensatina eschscholtzii salamander from the western United States is a classic example of allopatric speciation. In this tutorial, we demonstrate how GenGIS can be used to analyze non-linear geographic gradients (Parks and Beiko, 2009).

• Salamander tutorial
• Stream video tutorial
• Download salamander data set

Tutorial 5: Plugins

The functionality of GenGIS can be extended by writing a Python plugins. GenGIS comes with a number of Python plugins which can be accessed through the Plugins menu. Below is information about each of these plugins and instruction for developing your own plugin.

• Description of GenGIS plugins
• Creating a GenGIS plugin

Tutorial 6: Custom Data Visualizations and Movies

We have put together a number of examples illustrating how custom data visualizations and movies can be created using the API exposed to the Python console:

1. An example showing how GenGIS can be used to visualize the mobility rates of HIV-1 subtype B in Europe as proposed by Paraskevis et al. (2009) has been posted here. This example includes a Python class demonstrating how a custom visualization can be made.
2. Short examples of using the Python API to access data are available in the GenGIS manual.
3. Details on creating fly-through movies with GenGIS are available in the GenGIS manual.

References

Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R. 2009. Bacterial community variation in human body habitats across space and time. Science, 326: 1694-1697. (Abstract)

Parks DH and Beiko RG. 2009. Quantitative visualizations of hierarchically organized data in a geographic context. Geoinformatics 2009, Fairfax, VA. IEEE Xplore

Rusch DB, Halpern AL, Sutton G, et al. .2007. The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific. PLoS Biol. 5:e77. PubMed

Shapiro LH, Strazanac JS, and Roderick GK. 2006 Molecular phylogeny of Banza (Orthoptera: Tettigoniidae), the endemic katydids of the Hawaiian Archipelago. Mol. Phylogenet. Evol. 41:53-63. Pubmed