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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
It is developed by Stefan Karl (stefan[dot]karl[at]uni-wuerzburg[dot]de) at the Department of Bioinformatics of the University of Würzburg and supervised by Thomas Dandekar (head of the department).
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Jimena is available as a zip file (~0.9 MB, 26.02.15). It can be used as a GUI application, for example by double-clicking on the jimena.jar file (the executable flag must usually be set when using Linux), or as a library in your java project. We recommend using the library version for a better control of simulations and analyses. The source code is also included in the file.
The program and the source code are released under the GNU Lesser General Public License Version 3
Jimena requires Java 7 or above.
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 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.
The screenshot shows a simulation of the T-helper network in the Jimena GUI. The IL12 node was set to 1 between the time indices 1 and 2 by a perturbation and you can observe how the excitation propagates through the network.