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Biodiversity of 19 marine metagenomes from the Global Ocean Sampling expedition.

GenGIS (pronounced 'Genghis' like Genghis Khan) is a bioinformatics application that allows users to combine digital map data with information about biological sequences collected from the environment. GenGIS provides a 3D graphical 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.

Below you can find information about the software, data sources, tutorials, and the manual.

You can visit the gallery to see examples of what GenGIS can do.

GenGIS 2.3.0 has been released! See What's New for details.

  • New Feature: ShowSpread plugin to explore data over a variables extents.
  • New Feature: Polygons to cluster data over the levels of a field.
  • Improvement: Python on Windows is now version 2.7
  • Improvement: Locations can now be toggled from the properties menu, and on right click.
  • Improvement: Location Set Show/Hide All on right click.
  • Fixed: Linear Regression no longer requires sequence data.
  • Improvement: Gridding can now use the count(Sum) of string fields.


Getting Started

  • Visit the Github repository to get the source code, provide comments and submit pull requests.
  • Join our mailing list to keep informed about GenGIS developments
  • See our list of links for data and application support

Announcements

In addition to the mailing list and this page, GenGIS announcements are communicated by Rob Beiko (@rob_beiko) on Twitter.

  • (August 6, 2014) GenGIS v2.3.0 for Windows and OS X.
  • (April 17, 2014) GenGIS v2.2.2 for Windows and OS X.
  • (March 25, 2014) GenGIS v2.2.1 for Windows and OS X.
  • (December 17, 2013) GenGIS v2.2.0 for Windows and OS X.
  • (November 28, 2013) GenGIS v2.2.0 prerelease for Windows and OS X.
  • (August 7, 2013) GenGIS v2.1.1 release for Windows and OS X.
  • (April 30, 2013) GenGIS v2.1.0 release for Windows and OS X.
  • (July 27, 2012) GenGIS v2.0.2 release for Windows and OS X.
  • (April 30, 2012) GenGIS v2.0.1 release for Windows and OS X.
  • (March 29, 2012) GenGIS v2.0.0 release for Windows and OS X. What's new in GenGIS 2.0?
  • (September 14, 2010) GenGIS v1.08 release for Windows and OS X. A list of new features and bug fixes can be found here.
  • (July 6, 2010) GenGIS places 2nd in the iEvoBio visualisation challenge.

Examples

We are building a gallery of example applications using GenGIS, including tracking of the 2009 H1N1 outbreak and the spread of HIV-1 subtype B in Europe.

Citing GenGIS

Please cite GenGIS if you use it in your work. Currently the best citation for GenGIS is:

Parks DH, Mankowski T, Zangooei S, Porter MS, Armanini DG, Baird DJ, Langille MGI, Beiko RG. 2013. GenGIS 2: Geospatial analysis of traditional and genetic biodiversity, with new gradient algorithms and an extensible plugin framework. PLoS One, 8: 7, e69885. (Article)


Other papers and conference proceedings related to GenGIS:

  • Parks DH, Porter M, Churcher S, Wang S, Blouin C, Whalley J, Brooks S and Beiko RG. 2009. GenGIS: A geospatial information system for genomic data. Genome Research, 19: 1896-1904. (Abstract)
  • Parks DH, MacDonald NJ, and Beiko RG. 2009. Tracking the evolution and geographic spread of Influenza A. PLoS Currents: Influenza August 27:RRN1014. (Article)
  • Parks DH and Beiko RG. 2009. Quantitative visualizations of hierarchically organized data in a geographic context. Geoinformatics 2009, Fairfax, VA. Donovan won the best student paper award for his presentation. (Abstract)
  • Beiko RG, Whalley J, Wang S, Clair H, Smolyn G, Churcher S, Porter M, Blouin C, and Brooks S. 2008. Spatial analysis and visualization of genetic biodiversity. Free and Open Source Software for Geospatial (FOSS4G), Cape Town, South Africa (September-October 2008). (Abstract) (Full Paper)
  • Wang S, Beiko RG, and Brooks S. 2007. Collapsible 3D Terrains for GIS Visualization. Geovisualization, NUI Maynooth (September 2007). (Full Paper)

Contact Information

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

Funding of GenGIS

The development and deployment of GenGIS has been supported by several organizations:

Copyright

The text of this website is available for modification and reuse under the terms of the Creative Commons Attribution-Sharealike 3.0 Unported License and the GNU Free Documentation License (unversioned, with no invariant sections, front-cover texts, or back-cover texts).

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