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== GenGIS ==
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__NOTOC__
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[[Image:GOS_weighted_unifrac_full.png|thumb|right|400px|Biodiversity of 19 marine metagenomes from the [http://www.ncbi.nlm.nih.gov/pubmed/17355176 Global Ocean Sampling expedition].]]
  
GenGIS 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.
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GenGIS (pronounced 'Gengis' like with two hard 'g's) 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.
  
GenGIS version 1.0 is now available! Below you can find information about the software, data sources, tutorials, and the manual. The manual is still under development, but the tutorials and walkthroughs give a good overview of how to use the software.
 
  
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Below you can find information about the software, [[Data_sources|data sources]], [[GenGIS Tutorials|tutorials]], and the [[The GenGIS 2.3 Manual|manual]].
  
From here you can:
 
  
[[Download|Download GenGIS]]
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You can visit the [[Gallery|gallery]] to see examples of what GenGIS can do visually.
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For an overview of different analyses GenGIS can carry out, please visit the [[Description of GenGIS plugins|plugins page]].
  
[[Documentation|Visit the documentation page]] (Tutorials, manual, FAQ's)
 
  
[[Data_sources|See our list of links for data and application support]]
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'''GenGIS 2.5.3 has been released! See [[New in Version 2.5|What's New]] for details.'''
  
=== Citing GenGIS ===
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=== Getting Started ===
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* [[Download|Download GenGIS]] (Windows / Mac)
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* Visit the [https://github.com/beiko-lab/gengis Github repository] to get the source code, provide comments and submit pull requests.
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* [[Documentation|Documentation Page]] ([[GenGIS Tutorials|Tutorials]], [[The GenGIS 2.1 Manual|manual]], [[FAQ]])
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* Join our [http://ratite.cs.dal.ca/software_email_list mailing list] to keep informed about GenGIS developments
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* [[MapMaker|Download MapMaker]] (Provides easy access to maps compatible with GenGIS)
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* See our list of [[Data_sources|links]] for data and application support
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=== Announcements ===
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In addition to the mailing list and this page, GenGIS announcements are communicated by Rob Beiko (@rob_beiko) on Twitter.
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* (April 22, 2017) '''GenGIS v2.5.3 for Windows'''.
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* (March 9, 2016) '''GenGIS v2.5.0 for Windows'''.
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* (February 16, 2016) '''GenGIS v2.4.2 for Windows'''.
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* (August 27, 2015) '''GenGIS v2.4.1 for Windows and OS X'''.
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* (November 13, 2014) '''GenGIS v2.4.0 for Windows and OS X'''.
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* (August 6, 2014) '''GenGIS v2.3.0 for Windows and OS X'''.
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* (April 17, 2014) '''GenGIS v2.2.2 for Windows and OS X'''.
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* (March 25, 2014) '''GenGIS v2.2.1 for Windows and OS X'''.
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* (December 17, 2013) '''GenGIS v2.2.0 for Windows and OS X'''.
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* (November 28, 2013) '''GenGIS v2.2.0 prerelease for Windows and OS X'''.
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* (August 7, 2013) '''GenGIS v2.1.1 release for Windows and OS X'''.
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* (April 30, 2013) '''GenGIS v2.1.0 release for Windows and OS X'''.
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* (July 27, 2012) '''GenGIS v2.0.2 release for Windows and OS X'''.
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* (April 30, 2012) '''GenGIS v2.0.1 release for Windows and OS X'''.
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* (March 29, 2012) '''GenGIS v2.0.0 release for Windows and OS X'''. [[New Features in GenGIS 2.0|What's new in GenGIS 2.0?]]
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* (September 14, 2010) '''GenGIS v1.08 release for Windows and OS X'''. A list of new features and bug fixes can be found [[Revision History|here]].
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* (July 6, 2010) GenGIS places 2nd in the [http://ievobio.org/challenge.html iEvoBio visualisation challenge].
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* [[Previous announcements|Previous announcements]]
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=== Examples ===
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We are building a gallery of [[Gallery|example applications]] using GenGIS, including tracking of the [[H1N1|2009 H1N1 outbreak]] and the spread of [[HIV-1 subtype B mobility in Europe | HIV-1 subtype B in Europe]].
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== Citing GenGIS ==
  
 
Please cite GenGIS if you use it in your work. Currently the best citation for GenGIS is:
 
Please cite GenGIS if you use it in your work. Currently the best citation for GenGIS is:
  
'''Beiko, R., Whalley, J., Wang, S., Clair, H., Smolyn, G., Churcher, S., Porter, M., Blouin, C., & 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).''' ([http://www.osgeo.org/ocs/index.php/foss4g/2008/paper/view/105 Abstract]) ([[Media:Beiko_et_al_FOSS4G_Final.pdf|Full Paper]])
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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. ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0069885#pone-0069885-g005 Article])
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Other papers and conference proceedings related to GenGIS:
 
Other papers and conference proceedings related to GenGIS:
  
* Parks, D.H. and Beiko, R.G. (2009). Quantitative visualizations of hierarchically organized data in a geographic context. Accepted to ''Geoinformatics 2009'', Fairfax, VA.
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* 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. ([http://genome.cshlp.org/content/19/10/1896.abstract?sid=5fcec469-a13c-44f9-9f40-9e913e1c0ddf Abstract])
* Parks, D.H., Porter, M., Churcher, S., Wang, S., Blouin, C., Whalley, J., Brooks, S. and Beiko, R.G. GenGIS: A geospatial information system for genomic data. Currently submitted to ''Genome Research''. This will become the main GenGIS reference.
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* Parks DH, MacDonald NJ, and Beiko RG. 2009. Tracking the evolution and geographic spread of Influenza A. ''PLoS Currents: Influenza'' August 27:RRN1014. ([http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2762414.1/ Article])
* Wang, S., Beiko, R.G., & Brooks, S. (2007). Collapsible 3D Terrains for GIS Visualization. ''Geovisualization'', NUI Maynooth (September 2007). ([http://ncg.nuim.ie/geocomputation/sessions/6A/6A5.pdf Full Paper])
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* 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. ([http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?isnumber=5292806&arnumber=5293552&count=243&index=6 Abstract])
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* 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). ([http://www.osgeo.org/ocs/index.php/foss4g/2008/paper/view/105 Abstract]) ([[Media:Beiko_et_al_FOSS4G_Final.pdf|Full Paper]])
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* Wang S, Beiko RG, and Brooks S. 2007. Collapsible 3D Terrains for GIS Visualization. ''Geovisualization'', NUI Maynooth (September 2007). ([http://ncg.nuim.ie/geocomputation/sessions/6A/6A5.pdf Full Paper])
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== Contact Information ==
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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 [mailto:beiko@cs.dal.ca?Subject=GenGIS%20feedback 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.
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== Funding of GenGIS ==
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The development and deployment of GenGIS has been supported by several organizations:
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* [http://www.genomeatlantic.ca Genome Atlantic]
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* [http://www.genomecanada.ca Genome Canada] via the [http://ibarcode.org/steve/wordpress/ Biomonitoring 2.0 Project]
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* The Dalhousie Centre for Comparative Genomics and Evolutionary Bioinformatics, and the [http://www.tula.org/ Tula Foundation]
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* [http://www.nserc.ca The Natural Sciences and Engineering Research Council of Canada]
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* The Dalhousie [http://cs.dal.ca Faculty of Computer Science]
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== Copyright ==
  
=== Contact Information ===
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The text of this website is available for modification and reuse under the terms of the [http://en.wikipedia.org/wiki/Wikipedia:Text_of_Creative_Commons_Attribution-ShareAlike_3.0_Unported_License Creative Commons Attribution-Sharealike 3.0 Unported License] and the [http://en.wikipedia.org/wiki/Wikipedia:Text_of_the_GNU_Free_Documentation_License GNU Free Documentation License] (unversioned, with no invariant sections, front-cover texts, or back-cover texts).
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 (beiko [at] 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.
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Latest revision as of 17:44, 22 April 2017

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

GenGIS (pronounced 'Gengis' like with two hard 'g's) 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 visually. For an overview of different analyses GenGIS can carry out, please visit the plugins page.


GenGIS 2.5.3 has been released! See What's New for details.


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.

  • (April 22, 2017) GenGIS v2.5.3 for Windows.
  • (March 9, 2016) GenGIS v2.5.0 for Windows.
  • (February 16, 2016) GenGIS v2.4.2 for Windows.
  • (August 27, 2015) GenGIS v2.4.1 for Windows and OS X.
  • (November 13, 2014) GenGIS v2.4.0 for Windows and OS X.
  • (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).