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FBA Catalyst Deletion

This process is used to compute the effects of deleting sets of catalysts from a chemical reaction network. Note that a single catalyst may catalyze multiple reactions. The following steps are executed during this process:

1. The next set of catalyst names contained in the specified catalyst deletion file are retrieved, and the fluxes of the reactions for which they are required are constrained to the interval [0, 0].
2. The specified objective function is optimized in the specified sense, or direction, and the results are written to the next line of the specified output file.
3. If another set of catalyst names is present in the catalyst deletion file, Steps 1 and 2 are repeated.

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


Required Keywords Possible Values
Process FBA Catalyst Deletion
Reaction File The name of an FBA Reaction File containing a stoichiometric network.
Reaction-Catalyst File The name of the file containing all reaction-catalyst associations. See Reaction-Catalyst Association Files for further information.
Catalyst Deletion File The name of a text file containing the names of the catalysts to be deleted. See Catalyst Name Files for further information.
Constraints File The name of a text file containing the user-defined flux constraints. See Constraints 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 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
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 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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