13C-labeling experiments consist of feeding the cell culture with defined 13C-substrates to fingerprint downstream metabolites with 13C-carbons. To complement the current platform, we sought to build an open-source MATLAB-based package (WUFlux) for metabolic flux analysis.ġ3C-MFA requires both experimental and modeling efforts (Fig. A more rigorous flux analysis requires 13C-MFA, which combines FBA with 13C isotopic tracing. Nevertheless, the MicrobesFlux platform still performs only FBA to estimate the flux values. This platform now includes 3192 species compared to 1304 species in the previous version. The new MicrobesFlux has been updated with both AMPL optimization software and metabolic network information from the latest version of the KEGG database. Based on users’ feedback, we have re-built our system on a commercial server to improve its functionality, stability, and robustness. This platform can automatically draft a metabolic model from the annotated microbial genome in the KEGG database. Our research group built a web-based platform named MicrobesFlux ( ). To facilitate the development of genome scale models, much software has been developed. FBA can unravel microbial metabolism based on the stoichiometry of the metabolic reactions as well as measurements of the inflow (substrate uptake) and outflow fluxes (biomass and product synthesis). Metabolic flux analyses, including flux balance analysis (FBA) and 13C metabolic flux analysis (MFA), are widely used to predict or measure in vivo enzyme reaction rates in microbes. We will continue documenting curated models of non-model microbial species and improving WUFlux performance. Open-source software for 13C-MFA, WUFlux, with a user-friendly interface and easy-to-modify templates, is now available at ( ). We have also illustrated how model constraints of cofactor and ATP balances influence fluxome results. To validate our model’s applicability, we have compared and discussed the flux results obtained from WUFlux and other MFA software. WUFlux also offers several ways of visualizing the flux results with respect to the constructed network. Users can modify the network and constraints, and then analyze the microbial carbon and energy metabolisms of various carbon substrates (e.g., glucose, pyruvate/lactate, acetate, xylose, and glycerol). To simplify 13C-MFA of different prokaryotic species, the software provides several metabolic network templates, including those for chemoheterotrophic bacteria and mixotrophic cyanobacteria. WUFlux is capable of directly correcting mass spectrum data of TBDMS (N-tert-butyldimethylsilyl-N-methyltrifluoroacetamide)-derivatized proteinogenic amino acids by removing background noise. Using GUIDE (graphical user interface design environment) in MATLAB, we built a user interface that allows users to modify models based on their own experimental conditions. We constructed an open-source platform for steady-state 13C-MFA. To facilitate and standardize the 13C-MFA modeling work, we set out to publish a user-friendly and programming-free platform (WUFlux) for flux calculations in MATLAB ®. Nonetheless, constructing the 13C-MFA model and performing flux calculation are demanding for new learners, because they require knowledge of metabolic networks, carbon transitions, and computer programming. Flux analyses, including flux balance analysis (FBA) and 13C-metabolic flux analysis ( 13C-MFA), offer direct insights into cell metabolism, and have been widely used to characterize model and non-model microbial species.
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