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Two prediction methods are implemented: flux balance analysis and metabolites producibility check (Feist and Palsson, 2008).
Additional file 2: Document with a full description and mathematical formulation of the implemented Flux Analysis methods.
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We thus implemented a flux variability analysis and added the results to the fluxes shown in Figure 4 and 5.
All algorithms have been implemented and flux identifiability is investigated for the network of the central metabolic pathways of a microorganism.
We implemented both Flux Balance Analysis (FBA) and Metabolite Producibility methods to predict growth phenotypes (see Methods).
To implement the flux ratio constraint at butyryl-CoA, a new f rPTB) :f rAAD_2) flux ratio constraint was created.
The FCT scheme implements a flux limiter by combining higher and lower order schemes so as not to produce overshoot or undershoot at the subsequent time step.
The parameter scaling constant α introduced during the compactification provides a way to implement numerical flux estimation with efficiency.
The system-wide analysis of branch points and split ratios is complemented by metabolite essentiality analysis, implemented using either flux-sum analysis or metabolite flux minimisation.
Kowalik et al. [8] implemented this upwind flux approximation and showed remarkable stability in simulating global tsunami propagation and run-up.
This possibility, for the first time implemented in a flux analysis software, can highly refine the modelling of the system.
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