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OpenFLUX: efficient modelling software for 13C-based metabolic flux analysis.

Lake-Ee Quek1, Christoph Wittmann, Lars K Nielsen

  • 1Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, QLD 4072, Australia. j.kromer@uq.edu.au.

Microbial Cell Factories
|May 5, 2009
PubMed
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OpenFLUX is a new software for 13C metabolic flux analysis, simplifying complex calculations. This tool enhances the design, computation, and interpretation of metabolic flux studies for systems biology and metabolic engineering.

Area of Science:

  • Systems biology
  • Metabolic engineering

Background:

  • Quantitative analysis of metabolic fluxes provides key insights into biological systems.
  • Metabolic flux analysis relies on tracer cultivation, mass spectrometry, and mathematical modeling.
  • A lack of suitable modeling software limits the application of metabolic flux analysis.

Purpose of the Study:

  • To develop a user-friendly and flexible software application for 13C metabolic flux analysis.
  • To enhance the speed and accuracy of flux calculations.
  • To facilitate model creation and analysis in metabolic flux studies.

Main Methods:

  • Development of OpenFLUX software based on the Elementary Metabolite Unit (EMU) framework.
  • Automatic generation of MATLAB-readable metabolite and isotopomer balances from spreadsheet-defined reaction networks.

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  • Integration of built-in gradient-based search, Monte Carlo algorithms, and user-defined algorithms for experimental design, parameter estimation, and sensitivity analysis.

    • Main Results:

    • OpenFLUX significantly enhances computation speed for flux calculations.
    • The software facilitates model creation through automatic parsing of metabolic networks.
    • Demonstrated user-friendliness and reliability in a microbial flux study, reproducing published data and quickly identifying optimum flux distributions.

    Conclusions:

    • OpenFLUX is a fast and accurate application for steady-state 13C metabolic flux analysis.
    • The software will greatly improve the design, calculation, and interpretation of metabolic flux studies.
    • Open-source availability aims to foster the evolution of fluxomics research.