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FBA Constraint Variation-Reaction Deletion

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

1. If a constraints file is specified, the flux constraints it contains are applied.
2. An output file is opened with the next name specified in the output file name file.
3. The next set of flux constraints contained in the constraint variation file are applied. These constraints will override any pre-existing constraints.
4. The next set of reaction names contained in the specified reaction deletion file are retrieved, and the fluxes of their corresponding reactions are constrained to the interval [0, 0]. These constraints must not conflict with the current set of constraints from the constraint variation file, or else the process will halt prematurely.
5. The specified objective function is optimized in the specified direction, and the results are written to the next line of the current output file.
6. If another set of reaction names is present in the reaction deletion file, Steps 4 and 5 are repeated.
7. The current output file is closed, and the flux constraints are returned to the state achieved immediately after Step 1.
8. If another set of flux constraints is present in the constraint variation file, Steps 2-7 are repeated.

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 Constraint Variation-Reaction Deletion
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.
Reaction Deletion File The name of a text file containing the names of the reactions to be deleted. See Reaction Name Files for further information.
Objective Function The objective function to be optimized for each set of constraints and deletions. See FBA 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 File The name of the file containing the names of the files to which the computed values will be written. See File Name Files and FBA Multiple-Optimization Output Files for further information.
Data Headers The data headers of the specified output files. 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.
Zero Cutoff The amount by which fluxes can differ from zero, but still be considered equal to zero. See Zero Cutoffs 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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