Chair of Bioinformatics



    Jimena is a Java genetic regulatory network simulation framework which focuses on computational efficacy and a modularized architecture to facilitate the development and testing of new algorithms and models surrounding GRNs. It features

    • Network import from yED graph files (Example 1: Download (source), Example 2: Download)
    • Full support of the exponential interpolation model implemented in SQUAD
    • Full support of the polynomial interpolation models implemented in Odefy, including a significantly better implementation of the interpolation algorithm
    • Several discrete update schemes
    • Perturbation support in all models
    • Several algorithms for the search of steady stable states in all models (fully multithreaded)
    • In development: Network stability analyses, etc.

    It is developed by Stefan Karl (stefan[dot]karl[at]stud-mail[dot]uni-wuerzburg[dot]de) at the Department of Bioinformatics of the University of Würzburg and supervised by Thomas Dandekar (head of the department).

    Update 04.10.14 

    • Fixed a bug where duplicate stable states were not recognized
    • Multiple result windows can now be open at the same time
    • States (e.g. stable states) can now be copied (Ctrl+C) from any window (e.g. stable state search) and entered into the nodes window (Ctrl+V)
    • The charts window now exports the time sequence data as a tab-separated table (compatible with common spreadsheet software)
    • Network states can now be loaded from text files and saved to them
    • The user may now choose whether to include the discrete stable states in a random search for stable states
    • Stable states can now be exported to a file and to the clipboard

    Network input format

    Activating influences are modeled using the yED standard arrow tip, inhibiting influences using any other tip (e.g. a diamond). Boolean nodes are modeled using nodes with the captions AND, OR, NOT, &&, ||, !. Cf. the examples above.


    The screenshow shows a simulation of the T-helper network in the jIMENA GUI (which is not yet included in the release). The simulation was started from random values and the NFAT node was set to 1 between the time indices 1 and 2 by a perturbation.

    Large figure




    Jimena is available as a zip file (26.02.2015); [outdated version: zip file (version, Apr, 2014), zip file (~0.6 MB, 16.09.2013)]. It runs both on windows (win xp, 7 and 8) and LINUX (ubuntu and suse are recommended). It can be used as a GUI application, for example by double-clicking on the jimena.jar file, or as a library in your java project. We recommend using the library version for a better control of simulations and analyses. The current source code ( zip file 12M, 22.09.2014, recommended) is also available.

    The program and the source code are released under the GNU Lesser General Public License Version 3.

    Jimena requires Java 7 or above.

    Network can be edited with yed software (URL: http://www.yworks.com/en/products_yed_download.html). A local backup for education is available here: yed(windows), yed(linux).

    You can easily make the library available to your project by adding it to your Java classpath (Eclipse: Right click on the Java-Projekt | "Properties" | "Java Build Path" | "Libraries" | "Add External JAR..." or create a library directory as shown here). Two example files are included in the zip archive.

    We recommend reading the tutorial below which explains how to access Jimenas jar-file as a java library and how to use many of Jimena's essential funcions. A tutorial for the GUI is also available.


    Prof. Thomas Dandekar

    Dandekar group, Functional Genomics and Systems Biology department,
    Lehrstuhl für Bioinformatik
    Biocerter, University of Wuerzburg Am Hubland,
    D-97074 Würzburg
    Tel.: +49 (0)931 31 84551
    Fax: +49 (0)931 31 84552

    Mail: dandekar@biozentrum.uni-wuerzburg.de