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Constrained Reverse Reaction Flux Intervals

This process is used to compute the intervals of fluxes in a stoichiometric network after the fluxes of reversible reactions have been constrained, or capped. All reactions in the provided network must be irreversible, or else an error will be reported. An upper bound is first determined for each flux in the stoichiometric network by computing the maximum flux of each reaction r in the following way:

1. A set R is created that contains the reactions in the stoichiometric network that are the reverse of r.
2. The minimum value of Σ fi is computed and denoted as α, where fi denotes the flux of reaction ri in the set R.
3. Σ fi is contrained to the interval [α, α].
4. The maximum flux of r is computed and saved for later use.
5. The constraint on Σ fi is restored to its original value.

The values computed in Step 4 are then used to define the upper bound on their respective fluxes. The intervals of each flux are then computed by minimizing and maximizing the flux of each reaction. If the minimization or maximization problems prove to be unbounded, the flux bounds are denoted as -∞ or +∞, respectively.


Here is the set of keywords this process understands, along with a description of their possible corresponding values. See the command line documentation for more information about keyword-value pairs.


Required Keywords Possible Values
Process FBA Constrained Reverse Reaction Flux Intervals
Reaction File The name of an FBA Reaction File containing a stoichiometric network.
Constraints File The name of a text file containing the user-defined flux constraints. See Constraints Files for further information.
Program Solver The name of the program solver to be used to compute the flux intervals. See Program Solvers for further information.
Output File Name The name of the file to which the computed flux intervals will be written. See Single-Flux Interval Vector Files for further information.
Optional Keywords Possible Values
Data Headers The data headers of the specified output file. See Reaction Name Data Headers for further information.
Zero Cutoff The amount by which a computed lower bound can exceed a computed upper bound. See Zero Cutoffs for further information.
Constraint Tolerance The amount by which the linear program solver is allowed to violate the defined flux constraints. See Constraint Tolerances for further information.
Safety Level The safety level at which the optimizations will be performed. See Safety Levels for further information.
Program Solver Parameter File The name of the file containing parameters for the linear program solver. See Program Solver Parameter Files for further information.

Examples

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