GenGIS Tutorials

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

Tutorial 0: Construct a Custom Digital Elevation Maps (DEM)

Instructions on how to contruct a custom DEM using the data available from the GTOPO30 site is available here.

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. [1]. GenGIS will be used to investigate whether or not this phylogeny is related to the geography of the Hawaiian Islands.

• Download text tutorial

• Stream or download video tutorial (27 MB)

• Download katydid data set

Tutorial 2: Marine Microbial Communities from the Atlantic Seaboard

In this tutorial, we examine samples collected as part of the Global Ocean Sampling metagenomic survey [2] in order to investigate the influence of environmental factors on the composition of microbial communities from marine ecosystems.

• Stream or download video tutorial (21 MB)

• Download GOS data set

Tutorial 3: Building a Custom Data Visualizaiton

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.

References

[1] L. H. Shapiro, J. S. Strazanac, and G. K. Roderick. (2006) Molecular phylogeny of Banza (Orthoptera: Tettigoniidae), the endemic katydids of the Hawaiian Archipelago. Mol. Phylogenet. Evol. 41:53-63. Pubmed

[2] D. Rusch, A. Halpern, G. Sutton, et al., (2007) "The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific," PLoS Biol. 5:e77. PubMed