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Constraint Variation Mahadevan-Schilling Flux Intervals

This process is used to compute the Mahadevan-Schilling intervals of fluxes in a stoichiometric network [1]. All reactions in the provided network must be irreversible, or else an error will be reported. 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 for the specified fluxes (or linear combinations of fluxes).
3. The flux intervals are computed, and the results are written to the next line of the specified output file.
4. All flux constraints are restored to the state achieved immediately after Step 1.
5. If another set of flux constraints is present in the constraint variation file, Steps 2-5 are repeated.

The way in which flux intervals are computed in Step 3 is the same as that used in the Mahadevan-Schilling Flux Intervals process.

References

1. Mahadevan R., Schilling C. H. (2003) The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab. Eng., 5(4): 264-76.

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-Mahadevan-Schilling Flux Intervals
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.
Flux Cap File The name of a text file containing the flux caps for the specified stoichiometric network. See Flux Cap 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
Constraints File The name of a text file containing an initial set of flux constraints. See Constraints Files for further information.
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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