Graphical Interface

The following screenshot of the main window of TESD, shows three menus: Simulations, Graphics, and Help:

The Simulation menu helps you to select the model or load a setting file, and then run simulations.
The Graphic menu shows the simulation results in three different representations.


This menu contains all the graphical forms you need to set and run simulations:

On Line

This menu allows you to set the various parameters of the simulation step by step:

Online data entry form picture
Population Sizes
Population Copy Number Entry
Migration Entry
Entries window snapshot

Input file

This item can be used to load a previously-registered simulation parameter file. To find out more about this file see Files.


Once a simulation has been set or loaded, you can run it as many times as you wish. You should be aware that running a simulation can take a long time, since the time taken is proportional to the number of copies of transposable elements, the number and size of populations, the number of generations, etc.
You can allocate more resources on your computer to TESD by running it with the option -Xms128, which initializes the RAM memory usage to 128 or -Xms256, which sets a maximum RAM value 256. For example:
"java -Xms128 -Xmx256 -jar TESD.jar


Four graphics are provided to interpret the results of a simulation:


When you click on "Curves", a file chooser appears, allowing you to view your computer folders and select a .mea (mean) or .var (variance) file (see Files for further details). The "Curves" window, which pops up, tracks the evolution of the transposable element copy number mean (y axis) across generations (x axis) for each population, which are characterized by a distinct color label at the bottom of the graph area. You can zoom by dragging the mouse from the top left corner to the bottom right, and also use many features to customize your graph by clicking with the left button of your mouse in the graph area (Control + click on Mac). This enables you to change the labels or the ranges, export the graph as a picture, etc.


After the simulation, you can obtain the frequencies of transposable element insertions along the chromosomes of individuals.


See Animated Maps, in the next section, for an overview of what this looks like.

Maps is another more illustrative way of representing the means or variances. Populations are represented on a xy coordinate space as spheres with a diameter proportional to the transposable element copy number at each of the generations of the simulation. For long simulations, you can choose a longer generation interval; a map will then be drawn for each of these generations.
To allow you to set the various parameters, a Mapsettings window appears as follows:

First, choose the .mea or .var file in the text file.
The second line allows you to set the coordinates of the populations on the map by clicking on New Entry. A Coordinates editor then appears which allows you to assign the coordinates. If you are not interested in seeing the populations at specific locations, by default they are placed randomly in an array of possible positions depending on the number of populations.

You can save the coordinates and use them again in a subsequent Map representation by clicking on the Browse button.
Then select the generation interval number and the number of maps you want to see. The default interval is set to draw 11 maps.

Animated Map

This graphic provides an animated display of the maps.
The scroller can be used to view the map at a specific generation. Press the left or right button to play the animation backwards or forwards.