Difference between revisions of "GenGIS Tutorials"

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The simple way to obtain DEMs suitable for use in GenGIS is described [[Obtaining DEM from ORNL DAAC|here]]. An older set of instructions on how to manually contruct a custom DEM is available [[GTOP030 Tutorial|here]]. You can also obtain 2D maps compatible with GenGIS using [[MapMaker|MapMaker]].
 
The simple way to obtain DEMs suitable for use in GenGIS is described [[Obtaining DEM from ORNL DAAC|here]]. An older set of instructions on how to manually contruct a custom DEM is available [[GTOP030 Tutorial|here]]. You can also obtain 2D maps compatible with GenGIS using [[MapMaker|MapMaker]].
 
  
 
=== Tutorial 1: ''Banza'' Katydids of the Hawaiian Islands ===
 
=== Tutorial 1: ''Banza'' Katydids of the Hawaiian Islands ===
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[[Image:KaydidTutorialImage.jpg|thumb|Geophylogeny of ''Banza'' katydids from the Hawaiian Islands.|400px|right]]
 
[[Image:KaydidTutorialImage.jpg|thumb|Geophylogeny of ''Banza'' katydids from the Hawaiian Islands.|400px|right]]
  
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.
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In this tutorial, we consider the phylogenetic tree of ''Banza'' katydids (acoustic insects) from the Hawaiian Islands recently recovered by Shapiro ''et al.'', 2006. GenGIS will be used to investigate whether or not this phylogeny is related to the geography of the Hawaiian Islands.
  
 
* [[Media:GenGIS_Katydid_Tutorial.pdf|Download text tutorial]]
 
* [[Media:GenGIS_Katydid_Tutorial.pdf|Download text tutorial]]
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=== Tutorial 2: Marine Microbial Communities from the Atlantic Seaboard ===
 
=== 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.  
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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.  
  
 
* [[Media:GenGIS_GOS_Tutorial.swf|Stream]] or [[Media:GenGIS_GOS_Movie.zip|download]] video tutorial (21 MB)
 
* [[Media:GenGIS_GOS_Tutorial.swf|Stream]] or [[Media:GenGIS_GOS_Movie.zip|download]] video tutorial (21 MB)
  
 
* [[Media:GenGIS_GOS_Data.zip|Download GOS data set]]
 
* [[Media:GenGIS_GOS_Data.zip|Download GOS data set]]
 
  
 
=== Tutorial 3: Custom Data Visualizations and Movies ===
 
=== Tutorial 3: Custom Data Visualizations and Movies ===
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=== References ===
 
=== 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. [http://www.ncbi.nlm.nih.gov/pubmed/16781170 Pubmed]
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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. [http://www.ncbi.nlm.nih.gov/pubmed/16781170 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. [http://www.ncbi.nlm.nih.gov/pubmed/17355176 PubMed]
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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. [http://www.ncbi.nlm.nih.gov/pubmed/17355176 PubMed]

Revision as of 23:10, 1 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. GenGIS will be used to investigate whether or not this phylogeny is related to the geography of the Hawaiian Islands.

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.

Tutorial 3: 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. Here is a list of all API functions.
  2. A few short examples of using the API are available in the GenGIS manual.
  3. 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.
  4. A video showing the spread of the 2009 H1N1 influenza outbreak is available here along with all data and code used to create the video. The Python class demonstrates how the properties of location sites can be accessed and modified using the API.
  5. A video showing the spread of polymorphic amino acid sites during the 2009 H1N1 outbreak is available here. The included Python class demonstrates how how pie charts can be accessed and modified using the API.
  6. A video showing the geophylogeny of the 2009 H1N1 outbreak is available here. The included Python class demonstrates how geophylogenies can be accessed and modified using the API.

References

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

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