User:Alex

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Contents

Introduction

GenGIS is a free and open-source bioinformatics application that allows geographic data to be merged with information about biological sequences collected from the environment. It consists of a 3D graphical user interface in which the user can navigate and explore the data, as well as a Python interface that allows easy scripting of statistical analyses using the Rpy libraries.

The Aneides lugubris of Western California, on of the top hotspots on the planet for species diversity where 33 of 44 salamander species are endemic to the state.

Loading Data

The Salamander data consists of a 2D map (Cali.tiff), location data (Aneides_Locations_Filtered.csv) and a phylogenetic tree (Aneides_Filtered.tre). For basic information on using the GenGIS interface and loading data please see the Banza Katydid Tutorial.

Changing Visual Properties

The location set properties were selected to differentiate the data set my mtDNA clades. The properties of the phylogenetic display were selected to ensure maximum visibility of locations on the map. For further details on setting visual properties see the Banza Katydid or GOS tutorials.

Creating Cartograms

In order to create a cartogram from a location set loaded in GenGIS you require as a basis a map and location set as a minimum. Sequence files can also be used as metadata to transform the map. By default the count of samples at each location is used to transform the map, which defaults to one per location if no Sequence file is loaded. To create a cartogram right click the map loaded map layer and select the Cartogram tab from the properties menu. To fine tune the cartogram two operations are available Location Radius and Variable Multiplier. Location Radius adjusts the size of the grid cells the map is divided into when the cartogram is created. Variable Multiplier amplifies the value of populated grid cells by a X times multiple of the stored value. The Resize density option can also be used increase the run time of cartogram creation by decreasing the resolution by the specified percentage during creation time.

File:Aneides l15 m15.png
Figure 1. A cartogram created using Aneides lugubris and a Location Radius value of 15 and a Variable Multiplier of 5.

Contact Information

We encourage you to send us suggestions for new features. GenGIS is in active development and we are interested in discussing all potential applications of this software. Suggestions, comments, and bug reports can be sent to Rob Beiko (beiko@cs.dal.ca). If reporting a bug, please provide as much information as possible and, if possible, a simplified version of the data set which causes the bug. This will allow us to quickly resolve the issue.

References