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

Quek, Lake-Ee, Wittmann, Christoph, Nielsen, Lars K. and Kromer, Jens O. (2009) OpenFLUX: Efficient modelling software for 13C-based metabolic flux analysis. Microbial Cell Factories, 8 25.1-25.15. doi:10.1186/1475-2859-8-25


Author Quek, Lake-Ee
Wittmann, Christoph
Nielsen, Lars K.
Kromer, Jens O.
Title OpenFLUX: Efficient modelling software for 13C-based metabolic flux analysis
Formatted title
OpenFLUX: Efficient modelling software for 13C-based metabolic flux analysis
Journal name Microbial Cell Factories   Check publisher's open access policy
ISSN 1475-2859
Publication date 2009-05
Sub-type Article (original research)
DOI 10.1186/1475-2859-8-25
Open Access Status DOI
Volume 8
Start page 25.1
End page 25.15
Total pages 16
Editor Antonio Villaverde
Place of publication London, United Kingdom
Publisher BioMed Central
Collection year 2010
Language eng
Formatted abstract
Background
The quantitative analysis of metabolic fluxes, i.e., in vivo activities of intracellular enzymes and pathways, provides key information on biological systems in systems biology and metabolic engineering. It is based on a comprehensive approach combining (i) tracer cultivation on 13C substrates, (ii) 13C labelling analysis by mass spectrometry and (iii) mathematical modelling for experimental design, data processing, flux calculation and statistics. Whereas the cultivation and the analytical part is fairly advanced, a lack of appropriate modelling software solutions for all modelling aspects in flux studies is limiting the application of metabolic flux analysis.

Results
We have developed OpenFLUX as a user friendly, yet flexible software application for small and large scale 13C metabolic flux analysis. The application is based on the new Elementary Metabolite Unit (EMU) framework, significantly enhancing computation speed for flux calculation. From simple notation of metabolic reaction networks defined in a spreadsheet, the OpenFLUX parser automatically generates MATLAB-readable metabolite and isotopomer balances, thus strongly facilitating model creation. The model can be used to perform experimental design, parameter estimation and sensitivity analysis either using the built-in gradient-based search or Monte Carlo algorithms or in user-defined algorithms. Exemplified for a microbial flux study with 71 reactions, 8 free flux parameters and mass isotopomer distribution of 10 metabolites, OpenFLUX allowed to automatically compile the EMU-based model from an Excel file containing metabolic reactions and carbon transfer mechanisms, showing it's user-friendliness. It reliably reproduced the published data and optimum flux distributions for the network under study were found quickly (<20 sec).

Conclusion
We have developed a fast, accurate application to perform steady-state 13C metabolic flux analysis. OpenFLUX will strongly facilitate and enhance the design, calculation and interpretation of metabolic flux studies. By providing the software open source, we hope it will evolve with the rapidly growing field of fluxomics.

Keyword Bidirectional reaction steps
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ
Additional Notes Article number 25

 
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Created: Thu, 03 Sep 2009, 07:55:24 EST by Mr Andrew Martlew on behalf of Aust Institute for Bioengineering & Nanotechnology