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).
- 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.
Jimena is available as a zip file (26.02.2015); [outdated version: zip file (version, Apr, 2014), zip file (~0.6 MB, 16.09.2013)].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,
Tel.: +49 (0)931 31 84551
Fax: +49 (0)931 31 84552
- JavaBDD (GNU LGPL) by John Whaley (http://javabdd.sourceforge.net) is used as a BDD framework.
- Icons (GNU LGPL) by Oxygen Team (http://www.iconarchive.com/artist/oxygen-icons.org.html)
- Several known GRN models have been implemented in Jimena. Cf. the papers for a comprehensive list.
- Support by DFG (Da 208/12-1) is gratefully acknowledged.