> User's Guide > Flux Balance Analysis > Optimization | ||||||
FBA Reaction Deletion
This process is used to compute the effects of deleting sets of reactions in a stoichiometric network. This is not the same as deleting sets of catalysts, since a single catalyst can catalyze multiple reactions, and a single reaction can be catalyzed by multiple catalysts. The following steps are executed during this process:
Here is the set of keywords this process understands, along with a description of their possible corresponding values. |
Required Keywords | Possible Values |
Process | FBA Reaction Deletion |
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. |
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 | 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. |
ExamplesClick here for an example. |