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the user simply has to perform a single mouse click on the blue bar corre-
sponding to a particular amino acid fragment, which is then colored white.
Analogously, clicking on a white bar reactivates the corresponding fragment.
Fig. 5.4 FiatFlux desktop user interface for net flux computation
To compute net fluxes in the central carbon metabolism network, 13 C-
based metabolic flux analysis is applied within the netto module of FiatFlux.
Figure 5.4 shows its user interface, which allows for the detailed configuration
of the reaction network model prior to net flux computation: In the “Reac-
tions” frame (left), reactions can be included/excluded and their reversibility
be modified. Similarly, metabolites can be included/excluded from balancing
in the “Metabolites” frame (center). The “Flux Ratios” frame (right) contains
the relevant flux ratios as computed by the ratio module, which can also
be included/excluded via the user interface. Finally, the experimentally de-
termined reaction rates and other metabolic parameters have to be specified
in the “Extracellular fluxes” text field at the bottom of the netto window.
Then, having all required data available, flux distributions can be computed.
Thefluxratioscalculatedwithinthe ratio andthemassbalancesofthemetabo-
lites ofthe reactionnetworkbuild a linearequationsystem, which ismade math-
ematically accessible by transformation to matrix notation. If the equation
system is determined or even overly constrained, it is simply solved by a least
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