Skip to content
optStoic-minFlux/minRxn code for PMID: 26530953
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
data
info
.gitignore
LICENSE
README.md
baron.opt
cplex.opt
minFlux.gms
minFlux_output.txt
minRxn.gms
optStoic.gms
optStoic_output.csv

README.md

optstoic-gams

optStoic-minFlux/minRxn GAMS code. If you use this code in your work, please cite the following paper: Anupam Chowdhury and Costas D. Maranas, "Designing overall stoichiometric conversions and intervening metabolic reactions", Scientific Reports, 2015 (PMID: 26530953).

Requirement:

  1. GAMS (https://www.gams.com/)
  2. BARON solver
  3. CPLEX solver

Description:

  1. optStoic
  • An MINLP-based optimization procedure for identifying the optimal stoichiometry of a reaction subject to thermodynamic constraints, charge and elemental balance.
  1. minFlux or minRxn
  • An MILP procedure to identify pathway(s) that carry minimal flux or consist of minimal number of reaction that conform to the given reaction stoichiometry.

The reaction and metabolite IDs are derived from the KEGG database (http://www.genome.jp/kegg/).

You can’t perform that action at this time.