Home > metabolic-economics > Contents.m

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/liebermeister/metabolic-network-toolbox) SBMLtoolbox - SBML import / export (see http://sbml.org/Software/SBMLToolbox) SBtab toolbox - SBtab format (https://github.com/liebermeister/sbtab-matlab) Copyright (C) 2014 Wolfram Liebermeister <wolfram.liebermeister@gmail.com>

Generated on Fri 12-Feb-2016 20:18:22 by