Jimena

OverviewExample networksLibrary tutorialGUI tutorial

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 W├╝rzburg and supervised by Thomas Dandekar (head of the department).

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Download

Jimena is available as a zip file (~0.6 MB, 16.09.2013). 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 source code (~0.2 MB, 16.09.2013) is also available.

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). It can then be used as demonstrated in this example.

You can also use the ready-to-use Eclipse workspace which contains the the example file and the library.

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.

Acknowledgements

Screenshot

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.