TESD version 1.0

TESD, standing for Transposable Element Simulator Dynamics, is a scientific application developed by the Laboratoire de Biométrie et Biologie Evolutive (UMR CNRS 5558, Université Claude Bernard Lyon 1, France).

Based on " The dynamics of transposable elements in structured populations", Deceliere et al. (Genetics 2005, 169: 467-474) have developed the simulation core of TESD in an object-oriented fashion. TESD simulates the number of genomic TE copies in different populations across generations (according to the Island Model), using classical models of TE dynamics. The parameters of the models (transposition and excision rates, selection intensity, recombination rate, migration rate, population sizes and number of populations) are defined by the users.

To make it more user-friendly, TESD has a graphical interface. Users can set the various parameter values by using forms that ask questions. The results of the simulations are visualized thanks to built-in graphical tools, using the JFreeChart library.

TESD provides a complete application that allows modellers to implement other models of TE dynamics. TESD is implemented in Java, an object-oriented language that can be extended easily, and this means that TESD can be run on all Operating Systems (Linux, Mac, Windows, Solaris, etc.).

Downloading TESD

As TESD is a java application that uses JFreeChart libraries and JavaHelp Libraries, you will have to download the four following .jar files:

TESD.jar containing the actual TESD program
jcommon-1.0.0.jar and jfreechart-1.0.0.jar, the JFreeChart libraries
jh.jar, the library of JavaHelp 2

Starting TESD

No "installation" is required if you already have the Java Runtime Environment (version 1.4.2 or earlier) on your computer; if not, click here. In any cases, the four .jar files must be placed in the same directory for TESD to work properly. To start TESD, depending on your Operating System:

Windows : simply double click on the TESD.jar file
Mac : as above
Linux : in a console, at the directory containing the .jar files, enter : java -jar TESD.jar

TESD can also be used via a command line interface instead of the graphical one. This can be useful for experienced users planning, for example, to embed TESD in a script or to study its outputs with R. See the Help Files for more details.

Help Content

The Help Content of TESD can be downloaded here.

Sources

TESD sources can be downloaded here.
You are free to change the sources of TESD.

Copyright notice

TESD has been developed in collaboration with two major libraries that should be acknowledged both for their excellence and because they are used under copyright license:

JFreeChart and JCommon libraries are under the GNU Lesser General Public License (full text)
JavaHelp is under the Sun Microsystems, Inc. Binary Code License Agreement and supplemental license term for JavaHelp version 2.0 (full text)

Authors & Contacts

TESD was developed by Gregory Deceliere and Yann Letrillard at the Genomes & Populations team of Christian Biémont at the Laboratoire de Biologie et Biométrie Evolutive (UMR CNRS 5558, Université Claude Bernard Lyon 1, Villeurbanne, France).
If you encounter any problems or have any questions when using or developing TESD, please contact Christian Biémont.

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