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Flux Plasticity Analysis

This process is used to analyze the plasticity of fluxes in a collection of flux interval vectors. A flux is considered:

  • never-active if its interval is [0, 0].
  • potentially-active if its interval is [0, x], where x > 0.
  • always-active if its interval is [x, y], where x > 0 and y ≥ x.
  • plastic if its range is greater than zero.
  • rigid if its range equals zero.

For each vector of flux intervals supplied to this process, the number of fluxes in the above categories will be written to a specified output file. Additionally, the names of the reactions whose fluxes are never-active, potentially-active, and always-active can be recorded as well, for each flux interval vector.

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 Flux Plasticity Analysis
Reaction File The name of an FBA Reaction File containing a stoichiometric network.
Flux Interval File The name of the file containing the sets of flux intervals to be analyzed. See Multiple-Flux Interval Vectors Files for further information.
Zero Cutoff The amount by which values can differ from zero, but still be considered equal to zero. See Zero Cutoffs for further information.
Output File Name The name of the file to which the results of the analysis will be written. The i-th line in this file corresponds to the i-th vector of flux intervals in the input file.
Optional Keywords Possible Values
Always-Active Reaction File Name The desired name of the file to which the sets of always-active reactions will be written. The i-th line in this file corresponds to the i-th set of flux intervals in the input file.
Potentially-Active Reaction File Name The desired name of the file to which the sets of potentially-active reactions will be written. The i-th line in this file corresponds to the i-th set of flux intervals in the input file.
Never-Active Reaction File Name The desired name of the file to which the sets of never-active reactions will be written. The i-th line in this file corresponds to the i-th set of flux intervals in the input file.

Examples

Click here for an example.