PK V4 META-INF/PK V4EMETA-INF/MANIFEST.MFManifest-Version: 1.0 Ant-Version: Apache Ant 1.6.5 Created-By: 1.5.0_06-b05 (Sun Microsystems Inc.) Main-Class: IslandModelTest Class-Path: jfreechart-1.0.0.jar jcommon-1.0.0.jar jh.jar X-COMMENT: Main-Class will be added automatically by build PK V4 help_content/PK V4help_content/help_images/PK V4 projet_these/PK V4projet_these/es/PK V4projet_these/et/PK V4projet_these/ig/PK V4projet_these/ig/images/PK V4projet_these/rn/PK V4fIslandModelTest.class0M ()* (+ , -. /0 1 234 567 89:;<()VCodeLineNumberTableLocalVariableTablethisLIslandModelTest;main([Ljava/lang/String;)VfenetreLprojet_these/ig/MainFrame;eLjava/lang/Exception; arguments[Ljava/lang/String;titreLjava/lang/String;IsMoLprojet_these/et/IslandModel; SourceFileIslandModelTest.java .TESD, Transposable Elements Simulator Dynamicsprojet_these/et/Util_Islandsprojet_these/ig/MainFrame = >?-cmd@ AB CDE FGYThis Program run without any parameters for initial users or with -cmd for advanced usersH IJ(ch.randelshofer.quaqua.QuaquaLookAndFeelK LJjava/lang/ExceptionIslandModelTestjava/lang/Object3(Ljava/lang/String;ZLprojet_these/et/IslandModel;)VsetDefaultCloseOperation(I)Vjava/lang/Stringequals(Ljava/lang/Object;)Z consoleDOS0(Ljava/lang/String;Lprojet_these/ig/MainFrame;)Vjava/lang/SystemoutLjava/io/PrintStream;java/io/PrintStreamprintln(Ljava/lang/String;)Vjavax/swing/UIManagersetLookAndFeel!/*   XLYM*Y+,N--*2 Y+,N,+-  :MRU:,0 689#=.?9BBCEHMORUUSWW>9 WX !U"# M$%&'PK V4qAAhelp_content/TESD Identitag

TESD version 1.0

TESD, for Transposable Element Simulator Dynamics, is a scientific application developped under researches of the Population Genomic department of CNRS' "Laboratoire de Biologie et Biométrie Evolutive" (LBBE, UMR 5558, Université Claude Bernard Lyon 1, France).

On the basis of " The dynamics of transposable elements in structured populations ", (G. Deceliere, Genetics. 2005 Jan;169(1):467-74), Gregory Deceliere had developped the simulation core of TESD in an object oriented fashion that translates real life characters mediating such process from TEs to the population. In other words, TESD simulate the number of TEs copy number that variate in populations during numerous generations, controling this process from the molecular level to the individual, the population and finaly the populations levels.

In order to match a main aspiration to design an easy to use application, TESD was doted to a graphical interface. In that way, users can set various parameters at all the previous levels to shape a precise picture of a simulation by the way of forms asking questions. After TESD operates the simulation, the results can be visualized thanks to built-in graphical tools, using the JFreeChart library.

An other great purpose of TESD was to propose to modelers in TE's dynamics a complete application in wich they could be abble to implement other models of TE dynamic to meet more specific aspects of TEs dynamic. In this way, TESD was choosen to be in Java for two principal qualities: an objetc oriented language, able to be extended easily, and because it makes TESD capable to run under all Operating Systems (Linux, Mac, Windows, Solaris, etc. ...).
We only ask to eventual programmers to indicate us who they are (at the coordinates given in the "about" menu item of the help menu), firstly in order to provide them the sources, but also to centralize the evolution of the program.

At its 1.0 version, TESD contains one model, the Island Model, that integrates different structured populations interfering by migration.

Download of TESD

As a java application using JFreeChart libraries and JavaHelp Libraries, you have to download 4 following .jar files:

Launching of TESD

No "installation" is required. In any case, you must keep the 4 .jar files together in the same directory for TESD to work fully. Depending on your Operating System, you need to, on:

Copyright note

Identitag sources for tag-to-gene mapping can be downloaded here. Sources allowing to connect two Identitag databases for two different species can be downloaded here.

Reference

If you use Identitag in a published work, please cite the following reference:
Identitag, a relational database for SAGE tag identification and interspecies comparison of SAGE libraries. Keime C., Damiola F., Mouchiroud D., Duret L., Gandrillon O. BMC Bioinformatics 2004 Oct 6;5(1):143. [Pubmed] [Free full text on Biomed Central]

If you encounter some problems when using Identitag, please contact Céline Keime. Any comments or suggestions are welcome.
If you have problems or comments...

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PK V4 `}44(help_content/help_console_interface.html Console Interface

Console Interface

The console interface is another way experienced users can use TESD, and is also suitable for repeated use. You can start TESD from a terminal, and then send commands via the keyboard to run simulations.

Running the console interface of TESD:

Open the terminal of your Operating System.
For Windows, the DOS window is reached by clicking on Start > All programs > Accessories >
Then go to the directory containing the .jar files (using cd the path of the directory). The command is :
If you do not enter -cmd , you will start the graphical interface of TESD.

The menu of the console interface:

The menu of TESD is then displayed as follows:

Procedures

        [1]-Start the GUI (Graphical User Interface)
        [2]-File data entry mode
        [3]-Run
        [4]-Exit

Enter your choice :

Clicking on 1 will start the graphical interface.

File data entry mode

The second item in the console interface menu is used to set the .para file containing the parameters of the simualtion:

What is the name of the input file?

gives the complete path of the .para file. After checking the .para to make sure that there are no errors, and to set the parameters to the simulation core of TESD, you have to enter the output file name:

What is the name of the output file?

The menu then changes to allow you to go to the following step (running) or to choose another .para file.

Running a simulation using the console interface

By entering 3 , you opt to run a simulation. Now enter the number of simulations you want to do (1 or several in a single shot).

Number of simulations :

Confirm whether you want to run the simulation(s) immediately (this can be useful if the simulation last a long time).

Would you want to start the thread (y/n)?

When the simulations are finished, the menu is displayed again, and the output files are created in the folder containing the .para file. PK V4 vvhelp_content/help_files.html help_files

Files


This page describes the files produced by TESD.

The .para files


File of the simulation parameters.