mfapy: An open-source Python package for 13C-based metabolic flux analysis

• Published in: Metabolic engineering communications Vol. 13; p. e00177
• Main Authors: Matsuda, Fumio, Maeda, Kousuke, Taniguchi, Takeo, Kondo, Yuya, Yatabe, Futa, Okahashi, Nobuyuki, Shimizu, Hiroshi
• Format: Journal Article
• Language: English
• Published: Elsevier B.V 01.12.2021; Elsevier
• Subjects: 13C-based metabolic flux analysis; computer software; computers; Experimental design; extensibility; Full Length; metabolic flux analysis; Non-linear optimization; Open-source software; Python package; stable isotopes; system optimization; Open-source software; 13C-based metabolic flux analysis; Experimental design; Python package; Non-linear optimization
• ISSN: 2214-0301; 2214-0301
• DOI: 10.1016/j.mec.2021.e00177

13C-based metabolic flux analysis (13C-MFA) is an essential tool for estimating intracellular metabolic flux levels in metabolic engineering and biology. In 13C-MFA, a metabolic flux distribution that explains the observed isotope labeling data was computationally estimated using a non-linear optimization method. Herein, we report the development of mfapy, an open-source Python package developed for more flexibility and extensibility for 13C-MFA. mfapy compels users to write a customized Python code by describing each step in the data analysis procedures of the isotope labeling experiments. The flexibility and extensibility provided by mfapy can support trial-and-error performance in the routine estimation of metabolic flux distributions, experimental design by computer simulations of 13C-MFA experiments, and development of new data analysis techniques for stable isotope labeling experiments. mfapy is available to the public from the Github repository (https://github.com/fumiomatsuda/mfapy). •An open-source Python package, mfapy, is developed for 13C-MFA.•mfapy enables users to write Python codes for data analysis procedures of 13C-MFA.•mfapy has a flexibility and extensibility to support various data analysis procedures.•Computer simulations of 13C-MFA experiments is supported for experimental design.