OpenMebius: An Open Source Software for Isotopically Nonstationary 13C-Based Metabolic Flux Analysis
Figure 3
Representative Matlab code and structure of the metabolic model directory for isotopically nonstationary-13C-metabolic flux analysis using OpenMebius. (a) A metabolic model “model” is generated from information described in “TCA cycle model” directory by “Modelconfig” and “ConstEMUnetwork” functions. After loading time course mass spectrometry data in “Artificial data” directory, isotopic labeling data of carbon sources and an initial metabolic flux distribution are prepared. A metabolic flux distribution (“Flux”) is estimated by the “marquardt_inst” function using nonlinear optimization (Levenberg-Marquardt method). (b) Directory structure of the TCA cycle model. Configuration for simulating isotopic labeling, carbon source, and mass balance are described in MSReac.csv, Substrate.csv, and Mass_balance.csv, respectively. The simulated data directory includes a series of experimental data. Fluxes for biomass syntheses and product excretion, isotopic labeling information of substrate, metabolic concentrations of intracellular metabolite, and sampling times are described in efflux.csv, Substrate.csv, Initial_pool.csv, and Time_course.csv, respectively. Components.csv defines chemical elements in a mass fragment. A series of Abandance_list.csv are time course of isotopic labeling enrichment data. The “TCA cycle model” and online manual are available on web page (http://www-shimizu.ist.osaka-u.ac.jp/hp/en/software/OpenMebius.html).
