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Constraint (10) sets the lower bound flux for each reaction j to SSL j (an observed reference state lower bound, if the observation data is available) or zero, based on the value of the binary variable y j d.
Additional constraints are used to bound flux ranges.
Constraint (9) sets the upper bound flux capacity for each reaction j.
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(Step 2): A linear transformation from the expression of the phenotype-associated genes, to reactions' upper bound (maximal flux capacity) is applied ('Materials and methods').
Thus, once the gene to be switched off was selected, we identified its gene-protein reaction association and selected as zero its upper and lower bound in flux activity.
During the steady state, the bind flux is balanced by the unbind flux from the receptors.
In this, the median of gene expression values are used to bound the fluxes of each reaction in the model.
UB is the upper bound for the flux, and LB is the lower bound for the flux.
(2) For each model reaction i, use flux variability analysis [ 48] to identify a lower and upper flux bound α i * and β i * respectively, for which ZFBA=Z*FBA is feasible.
Each reaction had an upper and a lower bound on the flux it can carry.
At the same time the need to avoid gravitationally induced phase stratification in the header places a lower bound on mass flux.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com