ltcsCalculator

ltcsCalculator provides tools to find largest thermodynamic consistent sets of EFMs.

If you use this software please cite

Matthias P. Gerstl, Christian Jungreuthmayer, Stefan Müller, and Jürgen Zanghellini. (2016), Which sets of elementary flux modes form thermodynamically feasible flux distributions?. FEBS J, 283: 1782–1794. doi:10.1111/febs.13702

Table of Contents

Installation

Examples

[LTCS calculation](#ltcs calculation)

• ltcstool.pl
• ltcstool_clever.pl
• ltcstool_hotstart.pl
• ltcstool_hotstart_clever.pl
• calcLtcs

Installation

1. Download ltcsCalculator
2. The generic calcLtcs is written in C and can be compiled using gcc compiler by performing:

   cd ltcsCalculator
   make
   

   calcLtcs is then located in ltcsCalculator/bin
3. Perl scripts are located in folder scripts and can be executed without compilation. All perl scripts can be started with -h to see the help page.

Examples

Examples for all programs and scripts are located in the examples folder. To remove all produced files run clean_examples.sh.

LTCS calculation

This section describes tools that calculates LTCS. All scripts result in the same LTCS. However, I would recomment to use the _clever scripts, as it seems that they have a better performance.

ltcstool.pl

This perl script calculates LTCS by efmtool input files. To make it easier for the solver an intervall can be given, which is used to narrow the space of allowed objective value. Additional yield information can be given. But be careful to use an already normalized EFM set. This script DOES NOT check if the EFMs are normalized! For detailed information run ltcstool.pl -h.

ltcstool_clever.pl

This perl script calculates LTCS as well as ltcstool.pl, but it reduces the search intervall itself after timeout of cplex. An alternative timeout for cplex can be given as argument. Additional yield information can be given. See ltcstool.pl for or run ltcstool_clever.pl -h for more information.

ltcstool_hotstart.pl

This perl script calculates LTCS when given a LP file created by ltcstool.pl or ltcstool_clever.pl. The calculation method is the same as for ltcstool.pl. Run ltcstool_hotstart.pl -h for detailed information.

ltcstool_hotstart_clever.pl

This perl script further calculates LTCS when given a LP file created by ltcstool.pl or ltcstool_clever.pl. The calculation method is the same as for ltcstool_clever.pl. Run ltcstool_hotstart_clever.pl -h for detailed information.

calcLtcs

This C program calculates LTCS without considering concentrations. This tool only uses the reversibility information of the reactions in EFMs. For detailed information run calcLtcs without any argument