Files in the disk:
In this directory, table A.1 is given in the folder "AppendixA". Table C.1 is given in the folder "AppendixC". 
The "codes" directory consists of the matlab codes used through out the thesis. 
In "AppendixD" dynamic_odes_SL.m and solver_SL.m files are available.The codes solve the sitff differential equations of chapter 3.
In "AppendixE" efm_analysis. m file is available. The code selects the EFMs that all the elements of the key set participate and the common reactions are identified. The necessary input file of EFMs are also available in the folder.
In "AppendixF" the codes responsible for the reconstruction of the stoichiometric matrix, flux balance analyses (linear and quadratic programming), flux variability analysis are given.
reconstruction.m, fba_lp.m, fba_qp.m and fva.m files are given.
In "AppendixG" annotationtable.m and spa.m files are given. The codes are necessary for protein-protein interaction network reconstruction process. The input files are also supplied.
Hardware requirements:
Processor: Intel(R) Core(TM)2 CPU T7200 @2.00GHz
Software requirements:
Matlab 7.4.0 is used.
Windows Vista Home Premium
Memory (RAM) 2.00 GB
32-bit operating system

