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Contents

PURPOSE ^

MATLAB code for Metabolic Economics

SYNOPSIS ^

This is a script file.

DESCRIPTION ^

 MATLAB code for Metabolic Economics

 The toolbox is based on the Metabolic Network Toolbox and uses
 its functions and data structures. Main purposes are:

   o Compute economical flux distributions
   o Test if flux distributions are economical (and thermo-feasible)
   o Compute economic potentials in agreement with a given flux distribution
   o Realise an economical flux distribution by an enzyme-balanced kinetic model
   o Optimise the enzyme levels in a kinetic model, leading to an enzyme-optimal state

 Options for all functions are stored in common
 matlab structs called 'cba_options' and 'cba_constraints'.


 Main functions (in directory 'cba')

 Options
   cba_default_options     - Set options in data structures 'cba_options' and 'cba_constraints'

 Feasible flux distribution 
   cba_adjust_fluxes       - Correct a flux distribution by removing economically infeasible cycles

 Check flux distribution (based on different types of information given)
   cba_feasible_cycle      - Check economical flux distribution (non-beneficial cycle criterion)
   cba_feasible_efm        - Check economical flux distribution (given non-beneficial flux modes)
   cba_feasible_lp         - Check flux mode for EFA criteria; choose enzyme costs and thermodynamic forces

 Compute economic potentials given fluxes
   cba_homogeneous_cost    - Determine economic potentials from the principle of even enzyme cost

 Compute fluxes and economic potentials
   cba_economic_state            - Find fluxes, chemical and economic potentials satisfying FBA/EBA/CBA constraints
   cba_check               - Check flux mode, chem. pot. differences, and spec. flux costs for feasibility

 Enzyme-balanced kinetic models
   cba_reconstruct_model   - Reconstruct enzyme-balanced model from economical flux mode
   cba_economic_potentials - Compute economic potentials and their sensitivities in a kinetic model
   cba_check_model         - Check kinetic model for being in an enzyme-optimal state

 Further utility functions can be found in 'cba_utils'


 MATLAB Toolbox required:
   Metabolic Network Toolbox (https://github.com/wolframliebermeister/mnt)
   SBMLtoolbox    - SBML import / export  (see http://sbml.org/Software/SBMLToolbox)
   SBtab toolbox  - SBtab format (https://github.com/wolframliebermeister/sbtab-matlab)

 Copyright (C) 2014
 Wolfram Liebermeister  <wolfram.liebermeister@gmail.com>

CROSS-REFERENCE INFORMATION ^

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