Difference between revisions of "GenGIS Tutorials"

From The GenGIS wiki
Jump to: navigation, search
Line 23: Line 23:
 
* [[Media:GenGIS_GOS_Data.zip|Download GOS data set]]
 
* [[Media:GenGIS_GOS_Data.zip|Download GOS data set]]
  
=== Tutorial 3: The ''Ensatina eschscholtzii'' ring species ===
+
=== 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 | Body Location tutorial]]
 +
* [[Media:GenGIS_Costello_Data.zip|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).
 
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).
Line 31: Line 38:
 
* [[Media:GenGIS_Salamanders.zip|Download salamander data set]]
 
* [[Media:GenGIS_Salamanders.zip|Download salamander data set]]
  
=== Tutorial 4: Plugins ===
+
=== 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.
 
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.
Line 38: Line 45:
 
* [[Creating a GenGIS plugin | Creating a GenGIS plugin]]
 
* [[Creating a GenGIS plugin | Creating a GenGIS plugin]]
  
=== Tutorial 5: Custom Data Visualizations and Movies ===
+
=== 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:
 
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:
Line 47: Line 54:
  
 
=== References ===
 
=== 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. ([http://www.sciencemag.org/content/326/5960/1694.short Abstract])
  
 
Parks DH and Beiko RG. 2009. Quantitative visualizations of hierarchically organized data in a geographic context. ''Geoinformatics 2009'', Fairfax, VA. [http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?reload=true&isnumber=5292806&arnumber=5293552&count=243&index=6 IEEE Xplore]
 
Parks DH and Beiko RG. 2009. Quantitative visualizations of hierarchically organized data in a geographic context. ''Geoinformatics 2009'', Fairfax, VA. [http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?reload=true&isnumber=5292806&arnumber=5293552&count=243&index=6 IEEE Xplore]

Revision as of 12:19, 16 March 2012

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

Contents

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.

Tutorial 2: Marine Microbial Communities from the Atlantic Seaboard

In this tutorial, 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.

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.

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).

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.

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