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FBA Constraint Variation

This process is used to compute the effects of varying the flux constraints in a stoichiometric network. The following steps are executed during this process:

1. If a constraints file is specified, the flux constraints it contains are applied.
2. The next set of flux constraints contained in the constraint variation file are applied. These constraints will override any pre-existing constraints.
3. The specified objective function is optimized in the direction of the specified optimization sense, and the results are written to the next line of the specified output file.
4. If another set of flux constraints is present in the constraint variation file, Steps 2 and 3 are repeated.

Note: At the beginning of the process, the first set of flux constraints is considered to be the next set.

Here is the set of keywords this process understands, along with a description of their possible corresponding values.


Required Keywords Possible Values
Process FBA Constraint Variation
Reaction File The name of an FBA Reaction File containing a stoichiometric network.
Constraint Variation File The name of a text file containing the user-defined flux constraint variations. See Constraint Variation Files for further information.
Objective Function The objective function to be optimized for each set of constraints. See Objective Functions for further information.
Optimization Sense The sense, or direction, in which the optimal values will be computed. See Optimization Senses for further information.
Program Solver The name of the program solver to be used to compute the optimal values. See Program Solvers for further information.
Output File Name The name of the file to which the computed values will be written. See FBA Multiple-Optimization Output Files for further information.
Data Headers The data headers of the specified output file. See FBA Optimization Data Headers for further information.
Optional Keywords Possible Values
Constraints File The name of a text file containing an initial set of flux constraints. See Constraints Files 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 optimization 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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