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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. Before computing the intervals of each flux, the fluxes of reactions participating in steady state cycles are capped. The following steps are undertaken to compute these intervals:

1. The maximum flux is computed for each reaction for which a flux cap was provided.
2. For each flux determined to be unbounded in Step 1, its upper bound is defined using its flux cap.
3. The minimum flux of each reaction in the stoichiometric network is computed.
4. The maximum flux of each reaction in the stoichiometric network is computed.
5. The minimum and maximum fluxes from Steps 3 and 4 are written to the specified output file.

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 Mahadevan-Schilling Flux Intervals
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.
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
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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