GenGIS

Last updated
GenGIS
Developer(s) Donovan Parks, Mike Porter, Timothy Mankowski, Suwen Wang, Sylvia Churcher, Alex Keddy, Christian Blouin, Jacqueline Whalley, Stephen Brooks, Rob Beiko
Stable release
2.5.3 / 22 April 2017;6 years ago (2017-04-22)
Repository
Operating system Windows, Mac OS X
Type Bioinformatics
License GPL v3
Website kiwi.cs.dal.ca/GenGIS/Main_Page

GenGIS [1] merges geographic, ecological and phylogenetic biodiversity data in a single interactive visualization and analysis environment. A key feature of GenGIS is the testing of geographic axes that can correspond to routes of migration or gradients that influence community similarity. [2] Data can also be explored using graphical summaries of data on a site-by-site basis, as 3D geophylogenies, or custom visualizations developed using a plugin framework. Standard statistical test such as linear regression and Mantel are provided, and the R statistical language can be accessed directly within GenGIS. Since its release, GenGIS has been used to investigate the phylogeography of viruses and bacteriophages, bacteria, and eukaryotes.

Contents

See also

Related Research Articles

<span class="mw-page-title-main">Geographic information system</span> System to capture, manage and present geographic data

A geographic information system (GIS) consists of integrated computer hardware and software that store, manage, analyze, edit, output, and visualize geographic data. Much of this often happens within a spatial database, however, this is not essential to meet the definition of a GIS. In a broader sense, one may consider such a system also to include human users and support staff, procedures and workflows, the body of knowledge of relevant concepts and methods, and institutional organizations.

Phylogeography is the study of the historical processes that may be responsible for the past to present geographic distributions of genealogical lineages. This is accomplished by considering the geographic distribution of individuals in light of genetics, particularly population genetics.

<span class="mw-page-title-main">Geomatics</span> Geographic data discipline

Geomatics is defined in the ISO/TC 211 series of standards as the "discipline concerned with the collection, distribution, storage, analysis, processing, presentation of geographic data or geographic information". Under another definition, it consists of products, services and tools involved in the collection, integration and management of geographic (geospatial) data. It is also known as geomatic(s) engineering. Surveying engineering was the widely used name for geomatic(s) engineering in the past.

<span class="mw-page-title-main">Photogrammetry</span> Taking measurements using photography

Photogrammetry is the science and technology of obtaining reliable information about physical objects and the environment through the process of recording, measuring and interpreting photographic images and patterns of electromagnetic radiant imagery and other phenomena.

<span class="mw-page-title-main">Crime mapping</span>

Crime mapping is used by analysts in law enforcement agencies to map, visualize, and analyze crime incident patterns. It is a key component of crime analysis and the CompStat policing strategy. Mapping crime, using Geographic Information Systems (GIS), allows crime analysts to identify crime hot spots, along with other trends and patterns.

Geoinformatics is the science and technology that develop and use data, software, and computing facilities in the cyberinfrastructure ecosystem to address the needs of geosciences and related branches of science and engineering.

<span class="mw-page-title-main">Choropleth map</span> Type of data visualization for geographic regions

A choropleth map is a type of statistical thematic map that uses pseudocolor, meaning color corresponding with an aggregate summary of a geographic characteristic within spatial enumeration units, such as population density or per-capita income.

A GIS software program is a computer program to support the use of a geographic information system, providing the ability to create, store, manage, query, analyze, and visualize geographic data, that is, data representing phenomena for which location is important. The GIS software industry encompasses a broad range of commercial and open-source products that provide some or all of these capabilities within various information technology architectures.

Geographic information science or geoinformation science is a scientific discipline at the crossroads of computational science, social science, and natural science that studies geographic information, including how it represents phenomena in the real world, how it represents the way humans understand the world, and how it can be captured, organized, and analyzed. It is a sub-field of geography, specifically part of technical geography. It has applications to both physical geography and human geography, although its techniques can be applied to many other fields of study as well as many different industries.

Geovisualization or geovisualisation, also known as cartographic visualization, refers to a set of tools and techniques supporting the analysis of geospatial data through the use of interactive visualization.

<span class="mw-page-title-main">Spatial analysis</span> Formal techniques which study entities using their topological, geometric, or geographic properties

Spatial analysis is any of the formal techniques which studies entities using their topological, geometric, or geographic properties. Spatial analysis includes a variety of techniques using different analytic approaches, especially spatial statistics. It may be applied in fields as diverse as astronomy, with its studies of the placement of galaxies in the cosmos, or to chip fabrication engineering, with its use of "place and route" algorithms to build complex wiring structures. In a more restricted sense, spatial analysis is geospatial analysis, the technique applied to structures at the human scale, most notably in the analysis of geographic data. It may also be applied to genomics, as in transcriptomics data.

<span class="mw-page-title-main">Dasymetric map</span> Hybrid type of thematic map

A dasymetric map is a type of thematic map that uses areal symbols to visualize a geographic field by refining a choropleth map with ancillary information about the distribution of the variable. The name refers to the fact that the most common variable mapped using this technique has generally been population density. The dasymetric map is a hybrid product combining the strengths and weaknesses of choropleth and isarithmic maps.

<span class="mw-page-title-main">Heat map</span> Data visualization technique

A heat map is a 2-dimensional data visualization technique that represents the magnitude of individual values within a dataset as a color. The variation in color may be by hue or intensity.

<span class="mw-page-title-main">Thematic map</span> Type of map that visualizes data

A thematic map is a type of map that portrays the geographic pattern of a particular subject matter (theme) in a geographic area. This usually involves the use of map symbols to visualize selected properties of geographic features that are not naturally visible, such as temperature, language, or population. In this, they contrast with general reference maps, which focus on the location of a diverse set of physical features, such as rivers, roads, and buildings. Alternative names have been suggested for this class, such as special-subject or special-purpose maps, statistical maps, or distribution maps, but these have generally fallen out of common usage. Thematic mapping is closely allied with the field of Geovisualization.

Digital Earth is the name given to a concept by former US vice president Al Gore in 1998, describing a virtual representation of the Earth that is georeferenced and connected to the world's digital knowledge archives.

The Great Britain Historical GIS is a spatially enabled database that documents and visualises the changing human geography of the British Isles, although is primarily focussed on the subdivisions of the United Kingdom mainly over the 200 years since the first census in 1801. The project is currently based at the University of Portsmouth, and is the provider of the website A Vision of Britain through Time.

<span class="mw-page-title-main">Geography</span> Study of lands and inhabitants of Earth

Geography is a field of science devoted to the study of the lands, features, inhabitants, and phenomena of Earth. The first recorded use of the word γεωγραφία was as a title of a book by Greek scholar Eratosthenes. Geography is an all-encompassing discipline that seeks an understanding of Earth and its human and natural complexities—not merely where objects are, but also how they have changed and come to be. While geography is specific to Earth, many concepts can be applied more broadly to other celestial bodies in the field of planetary science. Geography has been called "a bridge between natural science and social science disciplines."

Quantitative geography is a subfield and methodological approach to geography that develops, tests, and uses mathematical and statistical methods to analyze and model geographic phenomena and patterns. It aims to explain and predict the distribution and dynamics of human and physical geography through the collection and analysis of quantifiable data. The approach quantitative geographers take is generally in line with the scientific method, where a falsifiable hypothesis is generated, and then tested through observational studies. This has received criticism, and in recent years, quantitative geography has moved to include systematic model creation and understanding the limits of their models. This approach is used to study a wide range of topics, including population demographics, urbanization, environmental patterns, and the spatial distribution of economic activity. The methods of quantitative geography are often contrasted by those employed by qualitative geography, which is more focused on observing and recording characteristics of geographic place. However, there is increasing interest in using combinations of both qualitative and quantitative methods through mixed-methods research to better understand and contextualize geographic phenomena.

<span class="mw-page-title-main">GIS and environmental governance</span> Tool for environmental management

Geographic information system (GIS) is a commonly used tool for environmental management, modelling and planning. As simply defined by Michael Goodchild, GIS is as "a computer system for handling geographic information in a digital form". In recent years it has played an integral role in participatory, collaborative and open data philosophies. Social and technological evolutions have elevated digital and environmental agendas to the forefront of public policy, the global media and the private sector.

Technical geography is the branch of geography that involves using, studying, and creating tools to obtain, analyze, interpret, understand, and communicate spatial information. The other two branches, human geography and physical geography, can usually apply the concepts and techniques of technical geography. However, the methods and theory are distinct, and a technical geographer may be more concerned with the technological and theoretical concepts than the nature of the data. Thus, the spatial data types a technical geographer employs may vary widely, including human and physical geography topics, with the common thread being the techniques and philosophies employed. To accomplish this, technical geographers often create their own software or scripts, which can then be applied more broadly by others. While technical geography mostly works with quantitative data, the techniques and technology can be applied to qualitative geography, differentiating it from quantitative geography. Within the branch of technical geography are the major and overlapping subbranches of geographic information science, geomatics, and geoinformatics.

References

  1. Parks, DH; Porter M; Churcher S; Wang S; Blouin C; Whalley J; Brooks S; Beiko RG (2009). "GenGIS: A geospatial information system for genomic data". Genome Research. 19 (10): 1896–1904. doi:10.1101/gr.095612.109. PMC   2765287 . PMID   19635847.
  2. Parks, DH; Beiko RG (2009). "Quantitative visualizations of hierarchically organized data in a geographic context". 2009 17th International Conference on Geoinformatics. Geoinformatics, Fairfax, VA. pp. 1–6. doi:10.1109/GEOINFORMATICS.2009.5293552. ISBN   978-1-4244-4562-2. S2CID   22986133.