Workflow of OpenFLUX. The software consists of 2 components (shaded box) – a JAVA-based metabolic model parser and a set of MATLAB-based algorithms for parameter estimation and sensitivity analysis. The user defines the reaction network in the model definition file, which contains the metabolic model and the experimental data input. The parser reads the metabolic model, and subsequently generates a metabolite balance model (stoichiometric matrix), and an isotopomer balance model using the EMU framework. The MATLAB-based computational algorithms use these models, in conjunction with the experimental data, to perform least-square parameter estimation and parameter sensitivity analysis. The optimized flux distributions and confidence intervals are obtained as results output.