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README.md

Steady-State-MFA

GS-MFA is a software program that is built to perform 13C-Metabolic flux analysis for large to genome-scale metabolic network. The scripts used the established methods described in MFA literature [1–4], summarized in Gopalakrishnan and Maranas, 2015 [5].

The program uses MATLAB as the platform and requires the following user-defined inputs: (i) metabolic model, (ii) atom mapping model, and (iii) labeling experiments. The program identifies the flux distribution that best recapitulates experimental labeling and extracellular flux input data and estimates flux 95% confidence interval.

Revised on Nov 14, 2019 Please cite the following for using the scripts Gopalakrishnan and Maranas. 2015. 13C metabolic flux analysis at a genome-scale. Metab Eng. 32:12-22. https://doi.org/10.1016/j.ymben.2015.08.006.

References

  1. Antoniewicz MR, Kelleher JK, Stephanopoulos G. Determination of confidence intervals of metabolic fluxes estimated from stable isotope measurements. Metab Eng. Academic Press; 2006;8: 324–337. doi:10.1016/J.YMBEN.2006.01.004
  2. Antoniewicz MR, Kelleher JK, Stephanopoulos G. Elementary metabolite units (EMU): A novel framework for modeling isotopic distributions. Metab Eng. Academic Press; 2007;9: 68–86. doi:10.1016/J.YMBEN.2006.09.001
  3. Crown SB, Long CP, Antoniewicz MR. Optimal tracers for parallel labeling experiments and 13C metabolic flux analysis: A new precision and synergy scoring system. Metab Eng. Academic Press; 2016;38: 10–18. doi:10.1016/J.YMBEN.2016.06.001
  4. Antoniewicz MR. A guide to 13C metabolic flux analysis for the cancer biologist. Exp Mol Med. Nature Publishing Group; 2018;50: 19. doi:10.1038/s12276-018-0060-y
  5. Gopalakrishnan S, Maranas CD. 13C metabolic flux analysis at a genome-scale. Metab Eng. Academic Press; 2015;32: 12–22. doi:10.1016/J.YMBEN.2015.08.006
  6. Burgard AP, Nikolaev E V., Schilling CH, Maranas CD. Flux coupling analysis of genome-scale metabolic network reconstructions. Genome Res. 2004;14: 301–312. doi:10.1101/gr.1926504

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Genome scale steady state 13C metabolic flux analysis

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