If no solution is attained, it is stated whether the reaction system is underdetermined or if no solution could be found that satisfied the defined quality criteria. 2.3. Emulation of User Interaction The user interactions required during the analysis process can be categorized into simple input of experimental data or the selection of modeling

parameters and more intricate user interactions targeted to the optimization of the calculations. Whereas the data input could simply be replaced in FiatFlux-headless by parameterized functions (see above), for the other steps the expert logic had to be translated into quantifiable criteria. The functions developed to emulate these tasks are packaged into the two

Inhibitors,research,lifescience,medical Inhibitors,research,lifescience,medical modules ratio_guiemulation and netto_guiemulation, respectively. In more detail, ratio_guiemulation contains the following subfunctions, which are applied in the given order: adjust_weights Exclude those amino acid fragments from the computation that are obsolete for the used labeling strategy and network model. remove_faulty_fragments If uniformly labeled glucose has been used, the fractional labeling of the analytes, which should reflect the fractional labeling value of the carbon source, is used as an additional quality criterion implemented in the function remove_faulty_fragments. Fractional Inhibitors,research,lifescience,medical labeling values that differ from the labeling fraction of the growth substrate by more than a user-defined percentage are not considered in the analysis (Default threshold is 15% deviation from Inhibitors,research,lifescience,medical the theoretical labeling fraction.) decrease_error To obtain flux ratios of high quality, faulty MDVAA have to be inhibitor Regorafenib excluded from the ratio calculation. In FiatFlux, the quality of the MS data is assessed by inspection of the fitting residuals of each MDVAA plotted on the GUI; fragments with

a high residual are inactivated by mouse click on the respective bar. This fragment selection process is automated Inhibitors,research,lifescience,medical in the function decrease_error. Amino acid fragments with fitting residuals exceeding a defined threshold value (default is 10−3) are categorized into unique fragments and redundant or equivalent fragments, hence, fragments with identical carbon backbone origin and theoretically identical MDVs. The most prominent amino acid fragments (denoted as m-15, m-57, m-85, m-159, Batimastat f302), which evolve due to the electron impact in the MS instrument, are used for the analysis. The fragments m-15 and m-57 contain the complete amino acid carbon chain, while m-85 and m-159 are lacking the carbon atom at position one [11]. Each of these pairs forms a group of equivalent fragments. Moreover, the carbon backbone of amino acids originating from a common precursor, for example L-phenylalanine and L-tyrosine, which are synthesized from prephenate, should be identical after the correction of naturally occurring isotopes.