Fig. 5

Example jQMM inputs and outputs for TCA toy model. The TCA toy model represents a symplification of the TCA cycle that still retains its main features and is used to test ¹³C MFA tools [35]. In this case, the input consists of the carbon transitions (the fate of each carbon for each the reaction), the feed labeling information (AcetylCoA 50% unlabeled, 25% labeled in the second carbon, 25% labeled in the first two carbons), the measured labeling patterns (glutamate MDVs), the error in these measurements, and the fluxes which are known (e.g. r6). File line examples are given in cursive below. In this case, all fluxes are assumed to be measured and the goal is to find the corresponding MDV for glutamate, which is given in the top right part of the figure (in red experimentally measured MDV, in blue theoretically calculated MDV). The lower right part of the figure provides a comparison with 13CFLUX2 [29], a well known ¹³C MFA package (See Jupyter Notebook B2)