regEfmtool: regulatory elementary flux mode tool

regEfmtool is a computational tool that combines the calculation of elementary flux modes in metabolic networks with transcriptional regulatory networks. regEfmtool is based on the open source software efmtool written by Marco Terzer. regEfmtool is an extension of the original efmtool that also considers (binary) transcriptional regulatory networks for the calculation of elementary flux modes. Specifically, regEfmtool only computes elementary flux modes, which are consistent with transcriptional regulation. As regulation excludes many of the mathematically possible elementary flux modes for biological reasons, regEfmtool allows to considerably reduce the computational cost of calculating elementary flux modes.

References

• Christian Jungreuthmayer, David E. Ruckerbauer, Matthias P. Gerstl, Michael Hanscho, and Jürgen Zanghellini. Avoiding the enumeration of infeasible elementary flux modes by including transcriptional regulatory rules in the enumeration process saves computational costs. PLOS one 10:e0129840 (2015). doi:10.1016/j.biosystems.2013.04.002
• Christian Jungreuthmayer, David E. Ruckerbauer, and Jürgen Zanghellini. regEfmtool: Speeding up elementary flux mode calculation using transcriptional regulatory rules in the form of three-state logic. Biosystems 113:37 (2013). doi:10.1016/j.biosystems.2013.04.002
• Christian Jungreuthmayer, David E. Ruckerbauer, and Jürgen Zanghellini. Utilizing gene regulatory information to speed up the calculation of elementary flux modes. arXiv:1208.1853 (2012). arxiv.org/pdf/1208.1853.pdf

Like the original efmtool, regEfmtool can be redistributed and used in source and binary forms, with or without modification, provided agreeing to the Simplified BSD License.

• Download and unzip regEfmtool
• Change to the newly created regEfmtool directory, e.g. 20120810_regEfmtool_2.0
• Read the provided README file
• Note that the package comes with a pre-compiled jar archive (hence, no compilation required)
• Change to the directory 'examples' and run the provided examples, e.g. start_regEfmtool_simple_1

Note that installation and usage of regEfmtool was only tested on Linux platforms. However, regEfmtool will most probably also run on other platforms, as it is a pure Java program. The pre-compiled package was built using JDK 1.7. If you experience problems running the example scripts, make sure that Java is installed on your system and that your PATH variable is set accordingly.

If you want to compile your own version of regEfmtool, then do the following:

• Change to the regEfmtool root directory created during the installation process
• Open the file 'Makefile' with your favorite editor
• Adapt the settings for JAR and JAVAC according to your system installation
• Save the changed Makefile
• Run 'make' to start compilation
• Run 'make jarfile' to create new regEfmtool jar package (note that this will remove the pre-complied jar package)
• Change to the example directory and run examples

Download

regEfmtool is available here: 20160114_regEfmtool_3.3.tar.gz.