Difference between revisions of "The GenGIS Manual"

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(File dependencies)
(File dependencies)
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Currently there are four types of files that can be imported directly by the GenGIS application (i.e., not via the Python console or Rpy):
 
Currently there are four types of files that can be imported directly by the GenGIS application (i.e., not via the Python console or Rpy):
  
- The digital map file
+
* The digital map file
- The location file
+
* The location file
- The sequence file
+
* The sequence file
- The phylogenetic tree file
+
* The phylogenetic tree file
  
 
Details of the requirements for these files are contained later in this section.
 
Details of the requirements for these files are contained later in this section.

Revision as of 19:26, 4 March 2009

A recent version of the manual is also available in Media:.PDF format.

Contents

Introduction / Overview of GenGIS

Purpose

Geography has always been an important component of evolutionary and ecological theory. But the advent of sequence typing approaches such as 16S ribotyping, DNA barcoding using the COX1 gene, and multi-locus sequence typing, gives us the opportunity to understand how communities of organisms interact, move around and evolve. This sequencing revolution is tightly coupled to the development of new algorithms for assessing and comparing populations based on their genes.

Coupled with these developments is the ready availability of high quality, public domain digital map data. By integrating molecular data with cartography and habitat parameters, we can visualize the geographic and ecological factors that influence community composition and function.

GenGIS is designed to bring these components together into a single software package that satisfies the following criteria:

Free and open source. GenGIS is released under a *** license, and we have made extensive use of other free packages such as wxWidgets, R, and Python. Making GenGIS freely available allows it to be downloaded and used anywhere in the world, and allows users to inspect and modify the source code.

User-friendly. Although GenGIS is built to deal with challenging scientific questions, our goal is to make the software as easy to use as possible. This is particularly important as many users will have little experience with digital map data, apart from applications such as Google Earth.

Adaptible and extensible. The principal strength of many open-source projects lies in the ability of a loosely organized community of users to develop and enhance the software: R and BioPerl are two examples of successful open-source projects with many contributors. Since the potential applications of GenGIS are much broader than those we have in mind, we aim to make it as easy as possible to extend its capabilities by exposing the internal data structures and offering a plugin architecture.

Platforms and System Requirements

GenGIS has been developed and tested on the following operating systems:

  • Win32 (XP and Vista)
  • Mac OSX 'Leopard'

Support for Linux is not a development priority at the moment, although it should in principle be difficult to port GenGIS to Linux, and we will happily support any efforts to develop such a version. Similarly, if you experience problems (or successes!) in trying to run GenGIS on an operating system not listed above.

GenGIS can have fairly demanding memory requirements, depending on the size of map that is loaded. ***General guidelines. Please note that we have not tested GenGIS on Windows with anything less than a Pentium 4-class CPU (Centrino, ***), nor on a Mac with anything older than a 2008-vintage iMac.

Citing GenGIS

The best citation for GenGIS will always be indicated in boldface on the [Main GenGIS page].

Where to go for help

The latest version of the GenGIS manual will always be available [here].

We maintain a [FAQ] for GenGIS as well.

      • Discussion forum
      • Email help

Installation

Getting the Release Version

If all you want to do is load in your data and start analyzing and visualizing them, your best bet is the latest Release version which is available [here].

Adding the Python Console

Adding R

Developer Version – building from source code

To build from source code, we currently use Microsoft Visual C++ Express ***version on Win32 platforms, and ***compiler on Mac.

Building on Windows

XXX

Building on Mac

XXX

Input data

File dependencies

Currently there are four types of files that can be imported directly by the GenGIS application (i.e., not via the Python console or Rpy):

  • The digital map file
  • The location file
  • The sequence file
  • The phylogenetic tree file

Details of the requirements for these files are contained later in this section.

We currently require that you load the map file first, followed by the location file, after which any properly formatted set of 1 or more sequence and/or tree files can be loaded. To be considered in a visual or statistical analysis, every sequence in a sequence file, and every leaf in a phylogenetic tree, must be associated with one of the locations in the Location file.

Maps

Supported formats

Projections

Data sources and GDAL

Typical limits on map size

Location File

Required fields

Location data – Lat / Long vs. UTM

Sequence File

Required fields

Other fields

Phylogenetic trees

File formats

Constraints / relationship with sequences

The Environment

The map environment

Map pane

Minimap

Getting around in GenGIS

Control elements

Hotkeys

Console input

Mouse

Menu options

Shortcut buttons

Interacting with sample sites

Working with Layers

Adding and removing

Active / inactive

wx Elements

Graphical analysis tools in GenGIS

Basic data visualizations

Pie charts

..?

2D phylogenetic trees

Defining axes

Manipulation

3D phylogenetic trees

The Python console and API functions

What you can do with the console

Accessing sample and sequence data

Capturing results

RPy and analyzing data

Installing R modules

Accessing sample data as tables in R

Capturing output from R

Implemented API functions (e.g. Mike's invocation of R charts)

Writing your own API functions