---------------------------------------------------------------
SUPPORTING INFORMATION 8:
DOCUMENTATION EXPLAINING ALL M-FILE CODES IN FOLDER
---------------------------------------------------------------

Author: Ahmad Abdullah Mannan (c)
E-mail: a.mannan@abdn.ac.uk *
Affiliation: Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7TE, UK.
Current Address: Institute for Complex Systems and Mathematical Biology, University of Aberdeen, King's College, Old Aberdeen, Aberdeen, AB24 3FX, UK.
Date: June 2014.

All files** contained in this folder are m-files, or MatLab readable files. The files contain scripts of the kinetic model itself, its parameters, and code for its analysis, to aid the reader in reproducing the results and figures. All files are reasonably well commented, with titles to parts of the calculations to explain and make plain to the reader what the functions are doing.


** The following files are declared to be owned by Ahmad Abdullah Mannan. The scripts may be edited by the reader, but they are not allowed to be re-distributed for money.


The m-files contained in this folder are as follows:

1) 'InitConds.m':
The initial conditions set for the kinetic model. These are also referred to as the Keio steady state metabolite concentrations, or Keio Phenotype (since it is a stable state), since they are mostly based on measured metabolite concentrations reported in the Keio multi-omics database from Ishii et al, 2007.

2) 'EColi_Parameters_StableKM.m':
Parameters used by the kinetic model.

3) 'EColi_StableKM_ContCult.m':
This is the kinetic model, after ensuring that the parameters of the model give us a stable Keio steady state, as described in the paper. This script contains all the reactions equations and the system of ODEs.

4) 'EColi_ContCult_NoGlcOrXDyn.m':
This is the kinetic model, same as (3), except that the dynamics of biomass and extraceullar glucose have been fixed to zero. This was done to ensure that we are able to find steady states in the same environmental and media conditions as that of the Keio steady state.

5) 'SystemJacobian.m':
Function for the calculation of the discrete form of the Jacobian of the kinetic model system, evaluated at a steady state.
This matrix is then used to calculate the eigenvalues of the system at the steady state of interest.

6) 'KineticModelAnalysis_ReproduceResultsInPaper.m':
This is the 'Master Code'. This code is self-contained and contains all functions and calculations that are used to reproduce the results and plots reported in the results section of the paper.