File 1 . OpenFLUX 2 : 13 C - MFA modeling software package adjusted for the comprehensive analysis of single and parallel labeling experiments
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OpenFLUX2: 13C-MFA modeling software package adjusted for the comprehensive analysis of single and parallel labeling experiments
BACKGROUND Steady-state (13)C-based metabolic flux analysis ((13)C-MFA) is the most powerful method available for the quantification of intracellular fluxes. These analyses include concertedly linked experimental and computational stages: (i) assuming the metabolic model and optimizing the experimental design; (ii) feeding the investigated organism using a chosen (13)C-labeled substrate (tracer...
متن کامل13CFLUX2—high-performance software suite for 13C-metabolic flux analysis
SUMMARY (13)C-based metabolic flux analysis ((13)C-MFA) is the state-of-the-art method to quantitatively determine in vivo metabolic reaction rates in microorganisms. 13CFLUX2 contains all tools for composing flexible computational (13)C-MFA workflows to design and evaluate carbon labeling experiments. A specially developed XML language, FluxML, highly efficient data structures and simulation a...
متن کاملFluxomers: A new approach for C metabolic flux analysis
Background: The ability to perform quantitative studies using isotope tracers and metabolic flux analysis (MFA) is critical for detecting pathway bottlenecks and elucidating network regulation in biological systems, especially those that have been engineered to alter their native metabolic capacities. Mathematically, MFA models are traditionally formulated using separate state variables for rea...
متن کاملOpenMebius: An Open Source Software for Isotopically Nonstationary 13C-Based Metabolic Flux Analysis
The in vivo measurement of metabolic flux by (13)C-based metabolic flux analysis ((13)C-MFA) provides valuable information regarding cell physiology. Bioinformatics tools have been developed to estimate metabolic flux distributions from the results of tracer isotopic labeling experiments using a (13)C-labeled carbon source. Metabolic flux is determined by nonlinear fitting of a metabolic model ...
متن کاملCatalytically Controlling the Reaction Pathways of Biomass-derived Oxygenate Molecules
Over the past 20 years, C-metabolic flux analysis (C-MFA) has emerged as the leading technology for accurate quantification of intracellular fluxes in microbial, mammalian and plant systems. Despite major advances in experimental, analytical and computational techniques, isotopic experiment design is often neglected for C-MFA. Optimal design of isotopic experiments is of central importance as i...
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تاریخ انتشار 2014