%***********************************************************************%
%  MATLAB PACKAGE FOR THE ARTICLE TITLED:
%  " Reconstruction and Flux Analysis of Coupling Between Metabolic
%    Pathways of Astrocytes and Neurons: Application to Cerebral Hypoxia"
%  
%  Article Authors: 
%  Tunahan Cakir, Selma Alsan, Hale Saybasili, Ata Akin, Kutlu O. Ulgen.
%
%***********************************************************************%

opt_brain.m: 
===========
main file performing FBA of resting condition and hypoxic states. Linear programming and quadratic programming is used. MATLAB interface to CLP solver   (http://www.coin-or.org/Clp/index.html,http://control.ee.ethz.ch/~joloef/clp.php) is used for solution of optimization problem.

opt_output.m
============
Used by opt_brain.m
reads the calculated flux distribution, and prints important fluxes/flux ratios into command window.

clp.m:
======
MATLAB interface to CLP solver. Coded by Johan Loefberg (http://control.ee.ethz.ch/~joloef/clp.php). Used for linear and quadratic programming. Requires mexclp.dll for functioning.

measdata.txt
============
Includes the names of reactions with measured flux, and corresponding upper and lower bounds of reaction fluxes for resting conditions. The text file is read by opt_brain.m.

measdata_HOX.txt
================
measurement constraints as explained above, but for hypoxic conditions. The text file is read by opt_brain.m.

brain_rxnlist_tbmm.txt
======================
Available in the subfolder 'text2mat'. Includes the list of compiled reactions for astrocyte and brain metabolism.

text2mat_brain.m
================
Available in the subfolder 'text2mat'. reads the reaction list from brain_rxnlist_tbmm.txt and constructs a stoichiometric matrix, with corresponding lower/upper bounds of reactions based on reaction reversibility. Also constructs cell arrays of metabolite and reaction names from the file.

coeff_met.m
===========
Available in the subfolder 'text2mat'. Used by text2mat_brain.m to read coefficients in front of each metabolite name.

func_metlist:
=============
Available in the subfolder 'text2mat'. Used by text2mat_brain.m to construct the list of metabolite names. 
