JMassBalance: mass-balanced randomization and analysis of metabolic networks

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JMassBalance.zip (3.7 MB)
Reference Manual (268 KB)
API Documentation View HTML

Last update: February 7, 2013

Installation instructions

Download JMassBalance.zip and extract the contained files to a local directory. Make sure that the Java Runtime Environment 1.6 or higher is installed by opening a command line window and typing java -version. The output should look similar to java version "1.6.0 11". Otherwise, install Java.

SBML Support

If you want to randomize SBML models, libSBML is required. For Windows, the files libsbmlj.jar and sbmlj.dll are included in the download package and provide SBML support without the need to install libSBML.

If you wish to use SBML models on Linux or Mac, libSBML has to be installed with Java support. Note that JMassBalance can also run without SBML support, so there is no need to install anything if you do not need SBML. Refer to Building and installing libSBML for installing libSBML with Java support on your system.

After the installation, replace the file libsbmlj.jar in the directory where you extracted the JMassBalance package by the file from the libSBML installation. On Linux, the latter is usually located at /usr/share/java/libsbmlj.jar. Additional steps may be required depending on your operating system. Refer to Making libSBML accessible to software for more information.

Running JMassBalance

JMassBalance can be used via a graphical user interface (GUI) or from the command line. The GUI is started by opening the file massbalance.jar with the Java Runtime Environment (java executable). Depending on your system configuration, this may be done by clicking the file or by executing

java -jar massbalance.jar

from the command line. For accessing all features of JMassBalance, such as parallelization, you should execute the program from the command line by typing

java -cp massbalance.jar massbalance/Randomize

Example:

The download package includes a toy network of the TCA cycle (file tca) and a compounds file with sum formulas (file tca.compounds). To generate 1000 mass-balanced randomized networks, execute the following command:

java -cp massbalance.jar massbalance/Randomize tca outdir massbalance

The directory outdir will be created, if it does not exist, and the log-files, mass equivalence classes and randomized networks will be placed therein.

After having generated the 1000 randomized networks, the characteristic path lengths of the TCA cycle and the randomized networks can be calculated by executing the following comand:

java -cp massbalance.jar massbalance/Properties tca outdir massbalance pathLength

The results are written to the file tca.0-999.massbalance.pathLength in the specified directory outdir. Note that, in order to calculate graph properties, you must specify an index range which is included in the index range of the previously randomized networks.

For more information, please refer to the Reference Manual.

Citation

If this software is useful for your work, please include one of the following references in your publication or redistribution:

Georg Basler and Zoran Nikoloski (2011): JMassBalance: mass-balanced randomization and analysis of metabolic networks. Bioinformatics, 27(19):2761-2762. doi:10.1093/bioinformatics/btr448

Georg Basler, Oliver Ebenhöh, Joachim Selbig, Zoran Nikoloski (2011): Mass-balanced randomization of metabolic networks. Bioinformatics, 27(10):1397-1403. doi:10.1093/bioinformatics/btr145