This folder contains nine files:

TCMC.m              -- Main script for TCMC estimation. It requires the 
                       user to install the freely available Systems 
                       Biology Toolbox 2 for Matlab (sbtoolbox).                          
                       Results are written in the "results" directory 
                       and its subdirectories. 

BIOMD0000000019.xml -- SBML file for the EGF/ERK Schroeberl model
                       available in the Biomodels database.

loadModel.m         -- Determines the full Schroeberl model, loads 
                       the model, and performs necessary 
                       initializations.

findWcond.m         -- Computes the Wegscheider conditions imposed 
                       by thermodynamics and generates the linear 
                       constraints matrix A.

findStartingKappa.m -- Computes a least-squares projection of the 
                       published parameters onto the feasible manifold.

simAnneal.m         -- Performs simulated annealing.

sqrErrCost.m        -- Computes the square error of a given set of 
                       parameters with respect to the experimental data 
                       provided in the original Schoeberl publication.

findEPRs.m          -- Computes and stores the entropy production rates  
                       associated with the reaction cycles.

makePlots.m         -- Plots the results of estimation.


The BioModels database can be accessed using the following link: 

http://www.ebi.ac.uk/biomodels-main


The Systems Biology Toolbox for Matlab can be accessed using the 
following link: 

http://www.sbtoolbox2.org/main.php