thermoEFM

thermoEFM is a matlab function for selecting the EFMs which are consistent with the equilibrium constant and the external concentrations of metabolites. The function has to be included in the with METATOOL directorie. It computes first all the EFMs of the model metatool and then select the thermodynamical EFMs. The parameters file must be an .xls file which contains two sheets : 'keq' for the equilibrium constants and 'ext' for the external metabolite concentrations.

Start your matlab program and cd into the directory where you have placed the files (or tell the program to include the directory in its search path). Then execute:

ex= thermoEFM('example.dat', 'parameters.xls');

This will read the input files and store the results into several fields of the data structure 'ex'. The input file is a .txt or .dat file describing the model. The format is the one of Metatool and it is described here : http://pinguin.biologie.uni-jena.de/bioinformatik/networks/metatool/metatool5.0/ecoli_networks.html The variable 'ex' (or whatever you choose to call it) is a structure that contains the metatool fields and two additional fields:

thermoEFMs list of thermodynamical EFMs
nonthermoEFMs list of non-thermodynamical EFMs



Moreover, you can draw all the thermodynamical EFMs:

drawThermo('example.dat','parameters.xls','example.xml','figure');

example.xml is a .xml file, representing the network, created with CellDesigner ( http://www.celldesigner.org/ ).
figure is the folder where the draws of efm are. WARNING it cannot be an empty string.
It will create figure folder. This folder will contain n files example_i.dat where n is the number of efm calculated by Metatool and i is a number between 1 and n.

Click here for the source code

Reference

Peres S, Jolicoeur M, Moulin C, Dague P and Schuster S.
submit to Plos One journal, december 2016.

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