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Next, we remove reactions that are involved in no identified metabolic pathway.
After an initial path is generated, our next step is to use proposal moves to add or remove reactions.
Ideally, OptKnock would operate by removing genes, not reactions, since it is not straightforward to independently remove reactions from a biological system without genetic manipulations.
FASTCC was run to remove reactions that are not able to carry a flux due to these additional medium constraints (Additional file 1: Figure S1).
Uptake reactions for metabolites not being present in the medium are shut down and FASTCC [ 28] is run to remove reactions that cannot carry a flux due to these additional constraints.
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The flow fields on these plates are pathways that both supply reactant and remove reaction products from the anode and cathode of a PEMFC.
Electrolyte is pumped through the system to deliver fresh solution to the anode and cathode as well as remove reaction byproducts.
The resultant brown precipitates were collected by suction filtration, Soxhlet-extracted with water for 3 days to completely remove reaction medium and then with methanol for three more days to get rid of unreacted pyrene and TMPBA.
For each subject, RTs were inverse transformed (to reduce the effect of outliers without the need to remove reaction time data points; Ratcliff 1993), and the mean for each condition was calculated.
In the second step, the set of candidate models is generated by removing reactions, species or modifiers and combinations thereof from the master model and/or by assigning alternative kinetics to certain reactions.
Removed reactions in the metabolic network of Portiera.
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