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Flux-P: Automating Metabolic Flux Analysis
Institute of Applied Microbiology (iAMB), RWTH Aachen University, Worringer Weg 1 52074 Aachen, Germany
Service and Software Engineering, University of Potsdam, August-Bebel-Straße 89, 14482 Potsdam, Germany
Programming Systems, TU Dortmund University, Otto-Hahn-Str. 14, 44227 Dortmund, Germany
These authors contributed equally to this work.
* Author to whom correspondence should be addressed.
Received: 4 September 2012; in revised form: 29 October 2012 / Accepted: 1 November 2012 / Published: 12 November 2012
Abstract: Quantitative knowledge of intracellular fluxes in metabolic networks is invaluable for inferring metabolic system behavior and the design principles of biological systems. However, intracellular reaction rates can not often be calculated directly but have to be estimated; for instance, via 13C-based metabolic flux analysis, a model-based interpretation of stable carbon isotope patterns in intermediates of metabolism. Existing software such as FiatFlux, OpenFLUX or 13CFLUX supports experts in this complex analysis, but requires several steps that have to be carried out manually, hence restricting the use of this software for data interpretation to a rather small number of experiments. In this paper, we present Flux-P as an approach to automate and standardize 13C-based metabolic flux analysis, using the Bio-jETI workflow framework. Exemplarily based on the FiatFlux software, it demonstrates how services can be created that carry out the different analysis steps autonomously and how these can subsequently be assembled into software workflows that perform automated, high-throughput intracellular flux analysis of high quality and reproducibility. Besides significant acceleration and standardization of the data analysis, the agile workflow-based realization supports flexible changes of the analysis workflows on the user level, making it easy to perform custom analyses.
Keywords: 13C metabolic flux analysis; MFA; high-throughput analysis; scientific workflows; workflow management; Bio-jETI
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Ebert, B.E.; Lamprecht, A.-L.; Steffen, B.; Blank, L.M. Flux-P: Automating Metabolic Flux Analysis. Metabolites 2012, 2, 872-890.
Ebert BE, Lamprecht A-L, Steffen B, Blank LM. Flux-P: Automating Metabolic Flux Analysis. Metabolites. 2012; 2(4):872-890.
Ebert, Birgitta E.; Lamprecht, Anna-Lena; Steffen, Bernhard; Blank, Lars M. 2012. "Flux-P: Automating Metabolic Flux Analysis." Metabolites 2, no. 4: 872-890.